From 295bbd997a752638f35c7a1066988034b53b2a3a Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 13 Sep 2021 12:29:55 -0400 Subject: [PATCH 1/7] Update README.rst --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index e6518f1..06004a0 100644 --- a/README.rst +++ b/README.rst @@ -39,7 +39,7 @@ Which have the following sub-commands: **Please read the USAGE** (https://genotype-variants.readthedocs.io/en/latest/usage.html) **section of the documentation for more information** -Requires GetBaseCountMultiSample v1.2.4 and above +Requires GetBaseCountMultiSample v1.2.5 and above To Do ----- From ace81b14ac4d25af8bc2712f332cc01f3d7cc183 Mon Sep 17 00:00:00 2001 From: buehlere Date: Wed, 20 Dec 2023 11:41:32 -0500 Subject: [PATCH 2/7] Dockerfile :heavy_check_mark: adding dockerfile --- .github/workflows/publish_docker.yaml | 64 +++++++++++++++++++++++++++ Dockerfile | 37 ++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 .github/workflows/publish_docker.yaml create mode 100644 Dockerfile diff --git a/.github/workflows/publish_docker.yaml b/.github/workflows/publish_docker.yaml new file mode 100644 index 0000000..7fed7a0 --- /dev/null +++ b/.github/workflows/publish_docker.yaml @@ -0,0 +1,64 @@ +name: Publish Docker image to ghcr.io +on: + push: + tags: + - "*" +jobs: + push_to_registries: + name: Build and publish Docker image + runs-on: ubuntu-latest + steps: + - name: Check out the repo + uses: actions/checkout@v3 + - name: Set up QEMU + uses: docker/setup-qemu-action@v2 + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v2 + - name: Prepare + # In this preparation step, a few configurations are made + # according to tags that will be used to export the image + # for Docker Hub, as well as the name of the image itself + id: prep + run: | + DOCKER_IMAGE=ghcr.io/msk-access/genotype_variants + VERSION=noop + if [ "${{ github.event_name }}" = "schedule" ]; then + VERSION=nightly + elif [[ $GITHUB_REF == refs/tags/* ]]; then + VERSION=${GITHUB_REF#refs/tags/} + elif [[ $GITHUB_REF == refs/heads/* ]]; then + VERSION=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g') + fi + TAGS="${DOCKER_IMAGE}:${VERSION}" + if [[ $VERSION =~ ^[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then + MINOR=${VERSION%.*} + MAJOR=${MINOR%.*} + TAGS="$TAGS,${DOCKER_IMAGE}:latest" + elif [[ $VERSION =~ ^v[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then + VERSION=$(echo ${VERSION#v}) + TAGS="${DOCKER_IMAGE}:${VERSION}" + elif [ "${{ github.event_name }}" = "push" ]; then + TAGS="$TAGS,${DOCKER_IMAGE}:sha-${GITHUB_SHA::8}" + fi + echo ::set-output name=version::${VERSION} + echo ::set-output name=tags::${TAGS} + - name: Login to GitHub Container Registry + #if: github.event_name != 'pull_request' + uses: docker/login-action@v2 + with: + registry: ghcr.io + username: ${{ github.repository_owner }} + password: ${{ secrets.RS_PAT }} + - name: Push to GitHub Packages + uses: docker/build-push-action@v3 + with: + context: . + file: ./Dockerfile + push: true + tags: ${{ steps.prep.outputs.tags }} + build-args: | + GENOTYPE_VARIANTS_VERSION=${{ steps.prep.outputs.version }} + labels: | + org.opencontainers.image.title=${{ github.event.repository.name }} + org.opencontainers.image.description=${{ github.event.repository.description }} + org.opencontainers.image.version=${{ steps.prep.outputs.version }} diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..6fcffac --- /dev/null +++ b/Dockerfile @@ -0,0 +1,37 @@ +################## Base Image ########## +ARG PYTHON_VERSION="3.8" +FROM --platform=linux/amd64 python:${PYTHON_VERSION}-slim + +################## ARGUMENTS/Environments ########## +ARG BUILD_DATE +ARG BUILD_VERSION +ARG LICENSE="Apache-2.0" +ARG GENOTYPE_VARIANTS_VERSION +ARG VCS_REF + +################## METADATA ######################## +LABEL org.opencontainers.image.vendor="MSKCC" +LABEL org.opencontainers.image.authors="Eric Buehler (buehlere@mskcc.org)" + +LABEL org.opencontainers.image.created=${BUILD_DATE} \ + org.opencontainers.image.version=${BUILD_VERSION} \ + org.opencontainers.image.licenses=${LICENSE} \ + org.opencontainers.image.version.pvs=${GENOTYPE_VARIANTS_VERSION} \ + org.opencontainers.image.vcs-url="https://github.com/msk-access/genotype_variants.git" \ + org.opencontainers.image.vcs-ref=${VCS_REF} + +LABEL org.opencontainers.image.description="This container uses python3.8 as the base image to build \ + genotype_variants ${GENOTYPE_VARIANTS_VERSION}" + +################## INSTALL ########################## + +WORKDIR /app +ADD . /app + +# get build tools and install genotype variants + +RUN apt-get update && apt-get install --no-install-recommends -y gcc g++ zlib1g-dev \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* \ + && pip install -r requirements_dev.txt \ + && python setup.py install From b0c0b86d30292d57aa9883f7c4737db8cf6d8b74 Mon Sep 17 00:00:00 2001 From: buehlere Date: Wed, 20 Dec 2023 11:42:31 -0500 Subject: [PATCH 3/7] fixing reqs and setup :heavy_check_mark: locking numpy version as newer versions clash with currently locked pandas version :heavy_check_mark: fixing some formatting in setup.py --- requirements_dev.txt | 1 + setup.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements_dev.txt b/requirements_dev.txt index 6e81dcb..77aea75 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -11,3 +11,4 @@ Click==7.0 click-log==0.3.2 pandas==1.0.0 xlrd==1.2.0 +numpy==1.19.2 diff --git a/setup.py b/setup.py index 52a6eb3..8341f9c 100644 --- a/setup.py +++ b/setup.py @@ -10,7 +10,7 @@ with open('HISTORY.rst') as history_file: history = history_file.read() -requirements = ['Click>=7.0', 'click_log>=version=0.3.2', 'pandas>=1.0.0', 'xlrd>=1.2.0'] +requirements = ['Click>=7.0', 'click_log>=0.3.2', 'pandas>=1.0.0', 'xlrd>=1.2.0'] setup_requirements = [ ] From 97da76822ae131bd3a5d08580c30ced47f879cef Mon Sep 17 00:00:00 2001 From: buehlere Date: Wed, 20 Dec 2023 11:54:37 -0500 Subject: [PATCH 4/7] cutting python version support python 3.5 and 3.6 are unstable versions, cutting support --- .github/workflows/validate.yaml | 4 ++-- .travis.yml | 2 -- setup.py | 2 +- 3 files changed, 3 insertions(+), 5 deletions(-) diff --git a/.github/workflows/validate.yaml b/.github/workflows/validate.yaml index f0569d7..6f24294 100644 --- a/.github/workflows/validate.yaml +++ b/.github/workflows/validate.yaml @@ -12,7 +12,7 @@ on: - 'docs/**' - '**.md' - '**.rst' - + jobs: test_nucleo: runs-on: ${{ matrix.platform }} @@ -21,7 +21,7 @@ jobs: max-parallel: 4 matrix: platform: [ubuntu-latest] - python-version: [3.5, 3.6, 3.7, 3.8] + python-version: [3.7, 3.8] steps: - name: Checkout repo uses: actions/checkout@v2 diff --git a/.travis.yml b/.travis.yml index bd650f5..dcac41d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,8 +4,6 @@ language: python python: - 3.8 - 3.7 - - 3.6 - - 3.5 # Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors install: pip install -U tox-travis diff --git a/setup.py b/setup.py index 8341f9c..c4e7534 100644 --- a/setup.py +++ b/setup.py @@ -19,7 +19,7 @@ setup( author="Ronak Shah", author_email='rons.shah@gmail.com', - python_requires='>=3.5', + python_requires='>=3.7', classifiers=[ 'Development Status :: 2 - Pre-Alpha', 'Intended Audience :: Developers', From fb83d1720d3ebe2c48810352fdf7a529302cd5e4 Mon Sep 17 00:00:00 2001 From: buehlere Date: Wed, 20 Dec 2023 11:57:54 -0500 Subject: [PATCH 5/7] Update tox.ini --- tox.ini | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/tox.ini b/tox.ini index d0d350e..de957be 100644 --- a/tox.ini +++ b/tox.ini @@ -1,12 +1,10 @@ [tox] -envlist = py35, py36, py37, py38, flake8 +envlist = py37, py38, flake8 [travis] python = 3.8: py38 3.7: py37 - 3.6: py36 - 3.5: py35 [testenv:flake8] basepython = python From 9828157c15f0ebefe4b9c4adbaf7a524888c4fe1 Mon Sep 17 00:00:00 2001 From: buehlere Date: Wed, 20 Dec 2023 12:05:57 -0500 Subject: [PATCH 6/7] Update test_genotype_variants.py incorrect method being used --- tests/test_genotype_variants.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_genotype_variants.py b/tests/test_genotype_variants.py index 3784b08..2f20fde 100644 --- a/tests/test_genotype_variants.py +++ b/tests/test_genotype_variants.py @@ -41,7 +41,7 @@ def test_merge_simplex_duplex(self): :return: """ - df_merge = small_variants.create_duplex_simplex_maf(self.s_maf, self.d_maf) + df_merge = small_variants.create_duplex_simplex_dataframe(self.s_maf, self.d_maf) df_merge = df_merge.sort_index() expected = pd.read_csv('tests/test_data/expected.maf', sep='\t') expected = expected.set_index(self.mutation_key, drop=False) From f1071519119dc6afe8d5386785a24e491d0712e8 Mon Sep 17 00:00:00 2001 From: buehlere Date: Tue, 16 Jan 2024 12:00:00 -0500 Subject: [PATCH 7/7] test re-write :heavy_check_mark: previous test had depreciated :heavy_check_mark: suspect handling of NA fill --- .gitignore | 1 + genotype_variants/create_all_maf_dataframe.py | 2 +- .../create_duplex_simplex_dataframe.py | 18 +- .../C-100000-L002-d02-DUPLEX_genotyped.maf | 11 + ...L002-d02-SIMPLEX-DUPLEX_genotyped copy.maf | 11 + ...0000-L002-d02-SIMPLEX-DUPLEX_genotyped.maf | 11 + .../C-100000-L002-d02-SIMPLEX_genotyped.maf | 11 + tests/test_data/expected.maf | 4 - tests/test_data/expected.tsv | 11 + tests/test_data/merged.tsv | 11 + tests/test_data/test_duplex.maf | 4 - tests/test_data/test_simplex.maf | 265 ------------------ tests/test_genotype_variants.py | 41 +-- 13 files changed, 105 insertions(+), 296 deletions(-) create mode 100644 tests/test_data/C-100000-L002-d02-DUPLEX_genotyped.maf create mode 100644 tests/test_data/C-100000-L002-d02-SIMPLEX-DUPLEX_genotyped copy.maf create mode 100644 tests/test_data/C-100000-L002-d02-SIMPLEX-DUPLEX_genotyped.maf create mode 100644 tests/test_data/C-100000-L002-d02-SIMPLEX_genotyped.maf delete mode 100644 tests/test_data/expected.maf create mode 100644 tests/test_data/expected.tsv create mode 100644 tests/test_data/merged.tsv delete mode 100644 tests/test_data/test_duplex.maf delete mode 100644 tests/test_data/test_simplex.maf diff --git a/.gitignore b/.gitignore index 4c915d1..d519969 100644 --- a/.gitignore +++ b/.gitignore @@ -104,3 +104,4 @@ ENV/ # IDE settings .vscode/ .idea/ +tests/.DS_Store diff --git a/genotype_variants/create_all_maf_dataframe.py b/genotype_variants/create_all_maf_dataframe.py index c872f0a..f44bf5a 100644 --- a/genotype_variants/create_all_maf_dataframe.py +++ b/genotype_variants/create_all_maf_dataframe.py @@ -368,7 +368,7 @@ def create_all_maf_dataframe( exit(1) logger.info("Successfully merged data frame") - + # fill NA for selected columns for returned df if df_o_s_ds is not None: return df_o_s_ds elif df_o_ds is not None: diff --git a/genotype_variants/create_duplex_simplex_dataframe.py b/genotype_variants/create_duplex_simplex_dataframe.py index a324f69..28ddf1a 100644 --- a/genotype_variants/create_duplex_simplex_dataframe.py +++ b/genotype_variants/create_duplex_simplex_dataframe.py @@ -1,6 +1,7 @@ import logging import numpy as np import sys +import pandas as pd """ create_duplex_simplex_dataframe @@ -237,6 +238,8 @@ def create_duplex_simplex_dataframe(simplex_dataframe, duplex_dataframe): exit(1) ##Add + cols_min = ["t_ref_count_fragment_simplex","t_ref_count_fragment_duplex", "t_alt_count_fragment_simplex", "t_alt_count_fragment_duplex"] + df_ds[cols_min] = df_ds[cols_min].replace(np.nan, 0) if df_ds.shape[0] > 0: try: df_ds["t_ref_count_fragment_simplex_duplex"] = ( @@ -258,7 +261,6 @@ def create_duplex_simplex_dataframe(simplex_dataframe, duplex_dataframe): + df_ds["t_ref_count_fragment_simplex_duplex"].astype(int) ) ).round(4) - df_ds["t_vaf_fragment_simplex_duplex"].fillna(0, inplace=True) logger.debug( "genotype_variants:small_variants:create_duplex_simplex_dataframe:: Successfully generated column for merged counts" ) @@ -274,7 +276,7 @@ def create_duplex_simplex_dataframe(simplex_dataframe, duplex_dataframe): df_ds["t_alt_count_fragment_simplex_duplex"] = [] df_ds["t_total_count_fragment_simplex_duplex"] = [] df_ds["t_vaf_fragment_simplex_duplex"] = [] - + # df_ds[cols].replace(0, np.nan, inplace=True) ##clean up try: df_ds.drop( @@ -333,4 +335,16 @@ def create_duplex_simplex_dataframe(simplex_dataframe, duplex_dataframe): logger.info( "Successfully merged data frame and the counts for simplex and duplex MAF" ) + # fill NA command for columns + cols = [ + "t_total_count_fragment_simplex", + "t_vaf_fragment_simplex", + "t_total_count_fragment_duplex", + "t_vaf_fragment_duplex", + "t_ref_count_fragment_simplex_duplex", + "t_alt_count_fragment_simplex_duplex", + "t_total_count_fragment_simplex_duplex", + "t_vaf_fragment_simplex_duplex", + ] + df_ds[cols] = df_ds[cols].replace(np.nan, 0) return df_ds diff --git a/tests/test_data/C-100000-L002-d02-DUPLEX_genotyped.maf b/tests/test_data/C-100000-L002-d02-DUPLEX_genotyped.maf new file mode 100644 index 0000000..5ff95cb --- /dev/null +++ b/tests/test_data/C-100000-L002-d02-DUPLEX_genotyped.maf @@ -0,0 +1,11 @@ +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count Caller t_total_count t_variant_frequency t_total_count_forward t_ref_count_forward t_alt_count_forward t_total_count_fragment t_ref_count_fragment t_alt_count_fragment +TERT mskcc.org GRCh37 5 1295233 1295262 + 5'Flank DEL CTGGGCCGGGGACCCGGGAGGGGTCGGGAC CTGGGCCGGGGACCCGGGAGGGGTCGGGAC GGGGGGNG C-100000-L002-d02-DUPLEX Normal UNPAIRED 260 0 1322 0 894 260 0 985 260 0 +TERT mskcc.org GRCh37 5 1295241 1295262 + 5'Flank DEL GGGACCCGGGAGGGGTCGGGAC GGGACCCGGGAGGGGTCGGGAC - C-100000-L002-d02-DUPLEX Normal UNPAIRED 284 0 1182 0 763 279 0 870 283 0 +TERT mskcc.org GRCh37 5 1295253 1295262 + 5'Flank DEL GGGTCGGGAC GGGTCGGGAC - C-100000-L002-d02-DUPLEX Normal UNPAIRED 324 0 928 0 529 317 0 723 321 0 +TERT mskcc.org GRCh37 5 1295261 1295262 + 5'Flank SNP AC AC CG C-100000-L002-d02-DUPLEX Normal UNPAIRED 356 0 734 0 342 329 0 638 344 0 +PMS2 mskcc.org GRCh37 7 6037055 6037056 + Splice_Site INS - - T C-100000-L002-d02-DUPLEX Normal UNPAIRED 1002 0 1016 0 650 650 0 903 897 0 +CDH1 mskcc.org GRCh37 16 68842732 68842732 + Missense_Mutation SNP A A C C-100000-L002-d02-DUPLEX Normal UNPAIRED 1999 3 2002 0.001498501515 924 922 2 1749 1747 2 +TP53 mskcc.org GRCh37 17 7579310 7579310 + Splice_Site SNP A A G C-100000-L002-d02-DUPLEX Normal UNPAIRED 1445 0 1445 0 727 727 0 1294 1294 0 +CD79B mskcc.org GRCh37 17 62007156 62007156 + Missense_Mutation SNP C C T C-100000-L002-d02-DUPLEX Normal UNPAIRED 0 0 0 0 0 0 0 0 0 0 +STK11 mskcc.org GRCh37 19 1219409 1219432 + Splice_Site DEL ACGGGTGCGTGCGCGGGGCAGGGG ACGGGTGCGTGCGCGGGGCAGGGG - C-100000-L002-d02-DUPLEX Normal UNPAIRED 548 0 1311 0 633 310 0 1199 547 0 +U2AF1 mskcc.org GRCh37 21 44513321 44513321 + Missense_Mutation SNP C C A C-100000-L002-d02-DUPLEX Normal UNPAIRED 0 0 0 0 0 0 0 0 0 0 diff --git a/tests/test_data/C-100000-L002-d02-SIMPLEX-DUPLEX_genotyped copy.maf b/tests/test_data/C-100000-L002-d02-SIMPLEX-DUPLEX_genotyped copy.maf new file mode 100644 index 0000000..a40eb70 --- /dev/null +++ b/tests/test_data/C-100000-L002-d02-SIMPLEX-DUPLEX_genotyped copy.maf @@ -0,0 +1,11 @@ +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer n_ref_count n_alt_count Caller t_total_count_fragment_simplex t_ref_count_fragment_simplex t_alt_count_fragment_simplex t_vaf_fragment_simplex t_ref_count_fragment_duplex t_alt_count_fragment_duplex t_total_count_fragment_duplex t_vaf_fragment_duplex t_ref_count_fragment_simplex_duplex t_alt_count_fragment_simplex_duplex t_total_count_fragment_simplex_duplex t_vaf_fragment_simplex_duplex +TERT mskcc.org GRCh37 5 1295233 1295262 + 5'Flank DEL CTGGGCCGGGGACCCGGGAGGGGTCGGGAC CTGGGCCGGGGACCCGGGAGGGGTCGGGAC GGGGGGNG C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 167 167 0 0.0 260 0 260 0.0 427 0 427 0.0 +TERT mskcc.org GRCh37 5 1295241 1295262 + 5'Flank DEL GGGACCCGGGAGGGGTCGGGAC GGGACCCGGGAGGGGTCGGGAC - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 185 185 0 0.0 283 0 283 0.0 468 0 468 0.0 +TERT mskcc.org GRCh37 5 1295253 1295262 + 5'Flank DEL GGGTCGGGAC GGGTCGGGAC - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 216 216 0 0.0 321 0 321 0.0 537 0 537 0.0 +TERT mskcc.org GRCh37 5 1295261 1295262 + 5'Flank SNP AC AC CG C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 236 236 0 0.0 344 0 344 0.0 580 0 580 0.0 +PMS2 mskcc.org GRCh37 7 6037055 6037056 + Splice_Site INS - - T C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 460 460 0 0.0 897 0 897 0.0 1357 0 1357 0.0 +CDH1 mskcc.org GRCh37 16 68842732 68842732 + Missense_Mutation SNP A A C C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 991 990 1 0.001 1747 2 1749 0.0011 2737 3 2740 0.0011 +TP53 mskcc.org GRCh37 17 7579310 7579310 + Splice_Site SNP A A G C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 1085 1085 0 0.0 1294 0 1294 0.0 2379 0 2379 0.0 +CD79B mskcc.org GRCh37 17 62007156 62007156 + Missense_Mutation SNP C C T C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 0 0 0 0.0 0 0 0 0.0 0 0 0 0.0 +STK11 mskcc.org GRCh37 19 1219409 1219432 + Splice_Site DEL ACGGGTGCGTGCGCGGGGCAGGGG ACGGGTGCGTGCGCGGGGCAGGGG - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 325 325 0 0.0 547 0 547 0.0 872 0 872 0.0 +U2AF1 mskcc.org GRCh37 21 44513321 44513321 + Missense_Mutation SNP C C A C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 26 26 0 0.0 0 0 0 0.0 26 0 26 0.0 diff --git a/tests/test_data/C-100000-L002-d02-SIMPLEX-DUPLEX_genotyped.maf b/tests/test_data/C-100000-L002-d02-SIMPLEX-DUPLEX_genotyped.maf new file mode 100644 index 0000000..a40eb70 --- /dev/null +++ b/tests/test_data/C-100000-L002-d02-SIMPLEX-DUPLEX_genotyped.maf @@ -0,0 +1,11 @@ +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer n_ref_count n_alt_count Caller t_total_count_fragment_simplex t_ref_count_fragment_simplex t_alt_count_fragment_simplex t_vaf_fragment_simplex t_ref_count_fragment_duplex t_alt_count_fragment_duplex t_total_count_fragment_duplex t_vaf_fragment_duplex t_ref_count_fragment_simplex_duplex t_alt_count_fragment_simplex_duplex t_total_count_fragment_simplex_duplex t_vaf_fragment_simplex_duplex +TERT mskcc.org GRCh37 5 1295233 1295262 + 5'Flank DEL CTGGGCCGGGGACCCGGGAGGGGTCGGGAC CTGGGCCGGGGACCCGGGAGGGGTCGGGAC GGGGGGNG C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 167 167 0 0.0 260 0 260 0.0 427 0 427 0.0 +TERT mskcc.org GRCh37 5 1295241 1295262 + 5'Flank DEL GGGACCCGGGAGGGGTCGGGAC GGGACCCGGGAGGGGTCGGGAC - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 185 185 0 0.0 283 0 283 0.0 468 0 468 0.0 +TERT mskcc.org GRCh37 5 1295253 1295262 + 5'Flank DEL GGGTCGGGAC GGGTCGGGAC - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 216 216 0 0.0 321 0 321 0.0 537 0 537 0.0 +TERT mskcc.org GRCh37 5 1295261 1295262 + 5'Flank SNP AC AC CG C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 236 236 0 0.0 344 0 344 0.0 580 0 580 0.0 +PMS2 mskcc.org GRCh37 7 6037055 6037056 + Splice_Site INS - - T C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 460 460 0 0.0 897 0 897 0.0 1357 0 1357 0.0 +CDH1 mskcc.org GRCh37 16 68842732 68842732 + Missense_Mutation SNP A A C C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 991 990 1 0.001 1747 2 1749 0.0011 2737 3 2740 0.0011 +TP53 mskcc.org GRCh37 17 7579310 7579310 + Splice_Site SNP A A G C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 1085 1085 0 0.0 1294 0 1294 0.0 2379 0 2379 0.0 +CD79B mskcc.org GRCh37 17 62007156 62007156 + Missense_Mutation SNP C C T C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 0 0 0 0.0 0 0 0 0.0 0 0 0 0.0 +STK11 mskcc.org GRCh37 19 1219409 1219432 + Splice_Site DEL ACGGGTGCGTGCGCGGGGCAGGGG ACGGGTGCGTGCGCGGGGCAGGGG - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 325 325 0 0.0 547 0 547 0.0 872 0 872 0.0 +U2AF1 mskcc.org GRCh37 21 44513321 44513321 + Missense_Mutation SNP C C A C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 26 26 0 0.0 0 0 0 0.0 26 0 26 0.0 diff --git a/tests/test_data/C-100000-L002-d02-SIMPLEX_genotyped.maf b/tests/test_data/C-100000-L002-d02-SIMPLEX_genotyped.maf new file mode 100644 index 0000000..64d2b3f --- /dev/null +++ b/tests/test_data/C-100000-L002-d02-SIMPLEX_genotyped.maf @@ -0,0 +1,11 @@ +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count Caller t_total_count t_variant_frequency t_total_count_forward t_ref_count_forward t_alt_count_forward t_total_count_fragment t_ref_count_fragment t_alt_count_fragment +TERT mskcc.org GRCh37 5 1295233 1295262 + 5'Flank DEL CTGGGCCGGGGACCCGGGAGGGGTCGGGAC CTGGGCCGGGGACCCGGGAGGGGTCGGGAC GGGGGGNG C-100000-L002-d02-SIMPLEX Normal UNPAIRED 167 0 801 0 553 167 0 628 167 0 +TERT mskcc.org GRCh37 5 1295241 1295262 + 5'Flank DEL GGGACCCGGGAGGGGTCGGGAC GGGACCCGGGAGGGGTCGGGAC - C-100000-L002-d02-SIMPLEX Normal UNPAIRED 185 0 705 0 466 184 0 543 185 0 +TERT mskcc.org GRCh37 5 1295253 1295262 + 5'Flank DEL GGGTCGGGAC GGGTCGGGAC - C-100000-L002-d02-SIMPLEX Normal UNPAIRED 216 0 557 0 337 211 0 454 216 0 +TERT mskcc.org GRCh37 5 1295261 1295262 + 5'Flank SNP AC AC CG C-100000-L002-d02-SIMPLEX Normal UNPAIRED 240 0 455 0 238 227 0 398 236 0 +PMS2 mskcc.org GRCh37 7 6037055 6037056 + Splice_Site INS - - T C-100000-L002-d02-SIMPLEX Normal UNPAIRED 493 0 543 0 361 361 0 490 460 0 +CDH1 mskcc.org GRCh37 16 68842732 68842732 + Missense_Mutation SNP A A C C-100000-L002-d02-SIMPLEX Normal UNPAIRED 1115 1 1118 0.0008944543661 609 608 0 993 990 1 +TP53 mskcc.org GRCh37 17 7579310 7579310 + Splice_Site SNP A A G C-100000-L002-d02-SIMPLEX Normal UNPAIRED 1201 0 1207 0 526 525 0 1089 1085 0 +CD79B mskcc.org GRCh37 17 62007156 62007156 + Missense_Mutation SNP C C T C-100000-L002-d02-SIMPLEX Normal UNPAIRED 0 0 0 0 0 0 0 0 0 0 +STK11 mskcc.org GRCh37 19 1219409 1219432 + Splice_Site DEL ACGGGTGCGTGCGCGGGGCAGGGG ACGGGTGCGTGCGCGGGGCAGGGG - C-100000-L002-d02-SIMPLEX Normal UNPAIRED 326 0 814 0 434 240 0 746 325 0 +U2AF1 mskcc.org GRCh37 21 44513321 44513321 + Missense_Mutation SNP C C A C-100000-L002-d02-SIMPLEX Normal UNPAIRED 27 0 28 0 9 9 0 27 26 0 diff --git a/tests/test_data/expected.maf b/tests/test_data/expected.maf deleted file mode 100644 index a33ce2b..0000000 --- a/tests/test_data/expected.maf +++ /dev/null @@ -1,4 +0,0 @@ -Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Sample_Barcode Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome.1 Start_Position.1 End_Position.1 Strand Variant_Classification Variant_Type Reference_Allele.1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode.1 Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count Caller t_total_count t_variant_frequency t_total_count_forward t_ref_count_forward t_alt_count_forward t_total_count_fragment Fillout_Type t_ref_count_fragment t_alt_count_fragment t_vaf_fragment summary_fragment -18 57571783 57571783 T - n_sample-CURATED-SIMPLEX-DUPLEX PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - n_sample-CURATED Normal UNPAIRED 266 3 301 0.00996678 210 207 0 520 CURATED-SIMPLEX 514 6 0.0115 DP=520;RD=514;AD=6;VF=0.0115 -18 48584855 48584855 A TTT n_sample-CURATED-SIMPLEX-DUPLEX SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT n_sample-CURATED Normal UNPAIRED 374 2 435 0.0045977 208 179 0 698 CURATED-SIMPLEX 694 4 0.0057 DP=698;RD=694;AD=4;VF=0.0057 -1 8080157 8080157 T A n_sample-CURATED-SIMPLEX-DUPLEX ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A n_sample-CURATED Normal UNPAIRED 430 0 524 0.0 293 200 0 1550 CURATED-SIMPLEX 1549 1 0.0006 DP=1550;RD=1549;AD=1;VF=0.0006 diff --git a/tests/test_data/expected.tsv b/tests/test_data/expected.tsv new file mode 100644 index 0000000..247c916 --- /dev/null +++ b/tests/test_data/expected.tsv @@ -0,0 +1,11 @@ +Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele2 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer n_ref_count n_alt_count Caller t_total_count_fragment_simplex t_ref_count_fragment_simplex t_alt_count_fragment_simplex t_vaf_fragment_simplex t_ref_count_fragment_duplex t_alt_count_fragment_duplex t_total_count_fragment_duplex t_vaf_fragment_duplex t_ref_count_fragment_simplex_duplex t_alt_count_fragment_simplex_duplex t_total_count_fragment_simplex_duplex t_vaf_fragment_simplex_duplex +5 1295233 1295262 CTGGGCCGGGGACCCGGGAGGGGTCGGGAC GGGGGGNG TERT mskcc.org GRCh37 5 1295233 1295262 + 5'Flank DEL CTGGGCCGGGGACCCGGGAGGGGTCGGGAC CTGGGCCGGGGACCCGGGAGGGGTCGGGAC GGGGGGNG C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 167 167 0 0.0 260 0 260 0.0 427 0 427 0.0 +5 1295241 1295262 GGGACCCGGGAGGGGTCGGGAC - TERT mskcc.org GRCh37 5 1295241 1295262 + 5'Flank DEL GGGACCCGGGAGGGGTCGGGAC GGGACCCGGGAGGGGTCGGGAC - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 185 185 0 0.0 283 0 283 0.0 468 0 468 0.0 +5 1295253 1295262 GGGTCGGGAC - TERT mskcc.org GRCh37 5 1295253 1295262 + 5'Flank DEL GGGTCGGGAC GGGTCGGGAC - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 216 216 0 0.0 321 0 321 0.0 537 0 537 0.0 +5 1295261 1295262 AC CG TERT mskcc.org GRCh37 5 1295261 1295262 + 5'Flank SNP AC AC CG C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 236 236 0 0.0 344 0 344 0.0 580 0 580 0.0 +7 6037055 6037056 - T PMS2 mskcc.org GRCh37 7 6037055 6037056 + Splice_Site INS - - T C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 460 460 0 0.0 897 0 897 0.0 1357 0 1357 0.0 +16 68842732 68842732 A C CDH1 mskcc.org GRCh37 16 68842732 68842732 + Missense_Mutation SNP A A C C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 991 990 1 0.001 1747 2 1749 0.0011 2737 3 2740 0.0011 +17 7579310 7579310 A G TP53 mskcc.org GRCh37 17 7579310 7579310 + Splice_Site SNP A A G C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 1085 1085 0 0.0 1294 0 1294 0.0 2379 0 2379 0.0 +17 62007156 62007156 C T CD79B mskcc.org GRCh37 17 62007156 62007156 + Missense_Mutation SNP C C T C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 0 0 0 0.0 0 0 0 0.0 0 0 0 0.0 +19 1219409 1219432 ACGGGTGCGTGCGCGGGGCAGGGG - STK11 mskcc.org GRCh37 19 1219409 1219432 + Splice_Site DEL ACGGGTGCGTGCGCGGGGCAGGGG ACGGGTGCGTGCGCGGGGCAGGGG - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 325 325 0 0.0 547 0 547 0.0 872 0 872 0.0 +21 44513321 44513321 C A U2AF1 mskcc.org GRCh37 21 44513321 44513321 + Missense_Mutation SNP C C A C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 26 26 0 0.0 0 0 0 0.0 26 0 26 0.0 diff --git a/tests/test_data/merged.tsv b/tests/test_data/merged.tsv new file mode 100644 index 0000000..e308c28 --- /dev/null +++ b/tests/test_data/merged.tsv @@ -0,0 +1,11 @@ +Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele2 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer n_ref_count n_alt_count Caller t_total_count_fragment_simplex t_ref_count_fragment_simplex t_alt_count_fragment_simplex t_vaf_fragment_simplex t_ref_count_fragment_duplex t_alt_count_fragment_duplex t_total_count_fragment_duplex t_vaf_fragment_duplex t_ref_count_fragment_simplex_duplex t_alt_count_fragment_simplex_duplex t_total_count_fragment_simplex_duplex t_vaf_fragment_simplex_duplex +5 1295233 1295262 CTGGGCCGGGGACCCGGGAGGGGTCGGGAC GGGGGGNG TERT mskcc.org GRCh37 5 1295233 1295262 + 5'Flank DEL CTGGGCCGGGGACCCGGGAGGGGTCGGGAC CTGGGCCGGGGACCCGGGAGGGGTCGGGAC GGGGGGNG C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 167 167 0 0.0 260 0 260 0.0 427 0 427 0.0 +5 1295241 1295262 GGGACCCGGGAGGGGTCGGGAC - TERT mskcc.org GRCh37 5 1295241 1295262 + 5'Flank DEL GGGACCCGGGAGGGGTCGGGAC GGGACCCGGGAGGGGTCGGGAC - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 185 185 0 0.0 283 0 283 0.0 468 0 468 0.0 +5 1295253 1295262 GGGTCGGGAC - TERT mskcc.org GRCh37 5 1295253 1295262 + 5'Flank DEL GGGTCGGGAC GGGTCGGGAC - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 216 216 0 0.0 321 0 321 0.0 537 0 537 0.0 +5 1295261 1295262 AC CG TERT mskcc.org GRCh37 5 1295261 1295262 + 5'Flank SNP AC AC CG C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 236 236 0 0.0 344 0 344 0.0 580 0 580 0.0 +7 6037055 6037056 - T PMS2 mskcc.org GRCh37 7 6037055 6037056 + Splice_Site INS - - T C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 460 460 0 0.0 897 0 897 0.0 1357 0 1357 0.0 +16 68842732 68842732 A C CDH1 mskcc.org GRCh37 16 68842732 68842732 + Missense_Mutation SNP A A C C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 991 990 1 0.001 1747 2 1749 0.0011 2737 3 2740 0.0011 +17 7579310 7579310 A G TP53 mskcc.org GRCh37 17 7579310 7579310 + Splice_Site SNP A A G C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 1085 1085 0 0.0 1294 0 1294 0.0 2379 0 2379 0.0 +17 62007156 62007156 C T CD79B mskcc.org GRCh37 17 62007156 62007156 + Missense_Mutation SNP C C T C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 0 0 0 0.0 0 0 0 0.0 0 0 0 +19 1219409 1219432 ACGGGTGCGTGCGCGGGGCAGGGG - STK11 mskcc.org GRCh37 19 1219409 1219432 + Splice_Site DEL ACGGGTGCGTGCGCGGGGCAGGGG ACGGGTGCGTGCGCGGGGCAGGGG - C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 325 325 0 0.0 547 0 547 0.0 872 0 872 0.0 +21 44513321 44513321 C A U2AF1 mskcc.org GRCh37 21 44513321 44513321 + Missense_Mutation SNP C C A C-100000-L002-d02-SIMPLEX-DUPLEX Normal UNPAIRED 26 26 0 0.0 0 0 0 0.0 26 0 26 0.0 diff --git a/tests/test_data/test_duplex.maf b/tests/test_data/test_duplex.maf deleted file mode 100644 index 534b8c3..0000000 --- a/tests/test_data/test_duplex.maf +++ /dev/null @@ -1,4 +0,0 @@ -Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Sample_Barcode Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count Caller t_total_count t_variant_frequency t_total_count_forward t_ref_count_forward t_alt_count_forward t_total_count_fragment t_ref_count_fragment_duplex t_alt_count_fragment_duplex Fillout_Type t_vaf_fragment summary_fragment -1 8080157 8080157 T A n_sample-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A n_sample-CURATED Normal UNPAIRED 1206 2 1371 0.00145879 960 795 2 1260 1140 1 CURATED-DUPLEX 0.0009 DP=1141;RD=1140;AD=1;VF=0.0009 -18 48584855 48584855 A TTT n_sample-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT n_sample-CURATED Normal UNPAIRED 374 2 435 0.0045977 208 179 0 406 347 2 CURATED-DUPLEX 0.0057 DP=349;RD=347;AD=2;VF=0.0057 -18 57571783 57571783 T - n_sample-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - n_sample-CURATED Normal UNPAIRED 266 3 301 0.00996678 210 207 0 289 257 3 CURATED-DUPLEX 0.0115 DP=260;RD=257;AD=3;VF=0.0115 diff --git a/tests/test_data/test_simplex.maf b/tests/test_data/test_simplex.maf deleted file mode 100644 index dad166d..0000000 --- a/tests/test_data/test_simplex.maf +++ /dev/null @@ -1,265 +0,0 @@ -Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Sample_Barcode Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count Caller t_total_count t_variant_frequency t_total_count_forward t_ref_count_forward t_alt_count_forward t_total_count_fragment t_ref_count_fragment_simplex t_alt_count_fragment_simplex Fillout_Type -1 8080157 8080157 T A sample_277-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_277-CURATED Normal UNPAIRED 320 2 413 0.00484262 271 178 2 378 308 1 CURATED-SIMPLEX -1 8080157 8080157 T A sample_278-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_278-CURATED Normal UNPAIRED 353 6 439 0.0136674 293 207 6 387 329 3 CURATED-SIMPLEX -1 8080157 8080157 T A sample_279-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_279-CURATED Normal UNPAIRED 457 0 581 0.0 388 265 0 530 432 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_280-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_280-CURATED Normal UNPAIRED 718 0 889 0.0 585 416 0 834 692 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_281-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_281-CURATED Normal UNPAIRED 307 5 386 0.0129534 261 182 5 361 296 3 CURATED-SIMPLEX -1 8080157 8080157 T A sample_282-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_282-CURATED Normal UNPAIRED 275 1 334 0.00299401 205 146 1 309 264 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_283-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_283-CURATED Normal UNPAIRED 337 1 387 0.00258398 243 193 1 351 316 1 CURATED-SIMPLEX -1 8080157 8080157 T A sample_284-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_284-CURATED Normal UNPAIRED 220 0 273 0.0 187 134 0 248 206 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_285-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_285-CURATED Normal UNPAIRED 617 1 787 0.00127065 506 337 1 729 597 1 CURATED-SIMPLEX -1 8080157 8080157 T A sample_286-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_286-CURATED Normal UNPAIRED 421 7 516 0.0135659 349 254 7 483 411 4 CURATED-SIMPLEX -1 8080157 8080157 T A sample_287-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_287-CURATED Normal UNPAIRED 680 1 813 0.00123001 532 400 1 730 632 1 CURATED-SIMPLEX -1 8080157 8080157 T A sample_288-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_288-CURATED Normal UNPAIRED 473 1 583 0.00171527 395 285 1 530 445 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_289-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_289-CURATED Normal UNPAIRED 336 9 416 0.0216346 282 202 9 394 324 6 CURATED-SIMPLEX -1 8080157 8080157 T A sample_290-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_290-CURATED Normal UNPAIRED 481 3 603 0.00497512 349 229 3 558 462 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_291-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_291-CURATED Normal UNPAIRED 156 1 169 0.00591716 112 99 1 153 143 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_292-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_292-CURATED Normal UNPAIRED 414 0 534 0.0 325 205 0 499 399 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_293-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_293-CURATED Normal UNPAIRED 356 1 401 0.00249377 271 226 1 357 328 1 CURATED-SIMPLEX -1 8080157 8080157 T A sample_294-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_294-CURATED Normal UNPAIRED 452 0 551 0.0 331 233 0 519 440 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_295-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_295-CURATED Normal UNPAIRED 397 3 471 0.00636943 316 242 3 443 384 2 CURATED-SIMPLEX -1 8080157 8080157 T A sample_296-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_296-CURATED Normal UNPAIRED 419 2 549 0.00364299 341 211 2 497 399 0 CURATED-SIMPLEX -1 8080157 8080157 T A n_sample-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A n_sample-CURATED Normal UNPAIRED 430 0 524 0.0 293 200 0 473 409 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_297-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_297-CURATED Normal UNPAIRED 220 2 244 0.00819672 183 159 2 233 213 1 CURATED-SIMPLEX -1 8080157 8080157 T A sample_298-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_298-CURATED Normal UNPAIRED 478 1 613 0.00163132 373 239 1 579 468 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_299-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_299-CURATED Normal UNPAIRED 272 0 334 0.0 214 152 0 313 260 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_300-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_300-CURATED Normal UNPAIRED 374 1 444 0.00225225 279 211 1 422 364 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_301-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_301-CURATED Normal UNPAIRED 373 0 494 0.0 281 162 0 457 363 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_302-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_302-CURATED Normal UNPAIRED 206 4 277 0.0144404 180 109 4 260 200 2 CURATED-SIMPLEX -1 8080157 8080157 T A sample_303-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_303-CURATED Normal UNPAIRED 371 3 466 0.00643777 308 214 3 420 350 2 CURATED-SIMPLEX -1 8080157 8080157 T A sample_304-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_304-CURATED Normal UNPAIRED 212 2 249 0.00803213 174 137 2 225 198 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_305-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_305-CURATED Normal UNPAIRED 272 0 323 0.0 198 147 0 290 254 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_306-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_306-CURATED Normal UNPAIRED 190 2 226 0.00884956 160 124 2 211 176 1 CURATED-SIMPLEX -1 8080157 8080157 T A sample_307-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_307-CURATED Normal UNPAIRED 382 0 462 0.0 286 206 0 441 374 0 CURATED-SIMPLEX -1 8080157 8080157 T A sample_308-CURATED ERRFI1 mskcc.org GRCh37 1 8080157 8080157 + Intron SNP T A sample_308-CURATED Normal UNPAIRED 388 0 461 0.0 310 238 0 435 375 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_585-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_585-CURATED Normal UNPAIRED 366 0 368 0.0 179 179 0 339 337 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_586-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_586-CURATED Normal UNPAIRED 475 0 476 0.0 238 237 0 438 437 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_587-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_587-CURATED Normal UNPAIRED 635 0 638 0.0 327 325 0 598 595 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_588-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_588-CURATED Normal UNPAIRED 831 0 835 0.0 422 420 0 764 761 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_589-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_589-CURATED Normal UNPAIRED 308 0 308 0.0 173 173 0 284 284 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_590-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_590-CURATED Normal UNPAIRED 331 0 331 0.0 178 178 0 305 305 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_591-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_591-CURATED Normal UNPAIRED 397 0 397 0.0 217 217 0 364 364 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_592-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_592-CURATED Normal UNPAIRED 254 0 254 0.0 139 139 0 239 239 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_593-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_593-CURATED Normal UNPAIRED 884 0 885 0.0 482 482 0 808 807 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_594-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_594-CURATED Normal UNPAIRED 461 0 461 0.0 240 240 0 419 419 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_595-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_595-CURATED Normal UNPAIRED 809 0 811 0.0 445 444 0 744 742 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_596-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_596-CURATED Normal UNPAIRED 579 0 581 0.0 280 278 0 532 530 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_597-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_597-CURATED Normal UNPAIRED 419 0 419 0.0 230 230 0 387 387 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_598-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_598-CURATED Normal UNPAIRED 566 0 570 0.0 306 305 0 528 524 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_599-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_599-CURATED Normal UNPAIRED 133 0 133 0.0 64 64 0 122 122 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_600-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_600-CURATED Normal UNPAIRED 451 0 456 0.0 227 225 0 413 409 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_601-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_601-CURATED Normal UNPAIRED 323 0 323 0.0 160 160 0 294 294 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_602-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_602-CURATED Normal UNPAIRED 431 0 432 0.0 246 245 0 395 394 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_603-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_603-CURATED Normal UNPAIRED 498 0 498 0.0 235 235 0 465 465 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_604-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_604-CURATED Normal UNPAIRED 604 0 607 0.0 318 316 0 563 560 0 CURATED-SIMPLEX -17 37882882 37882882 C A n_sample-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A n_sample-CURATED Normal UNPAIRED 447 0 450 0.0 222 220 0 407 405 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_605-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_605-CURATED Normal UNPAIRED 223 0 223 0.0 119 119 0 200 200 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_606-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_606-CURATED Normal UNPAIRED 607 0 608 0.0 318 317 0 569 569 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_607-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_607-CURATED Normal UNPAIRED 328 0 328 0.0 180 180 0 310 310 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_608-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_608-CURATED Normal UNPAIRED 414 0 416 0.0 232 232 0 391 389 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_609-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_609-CURATED Normal UNPAIRED 584 0 595 0.0 283 275 0 506 499 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_610-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_610-CURATED Normal UNPAIRED 214 0 215 0.0 125 124 0 197 196 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_611-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_611-CURATED Normal UNPAIRED 422 1 423 0.00236407 223 222 1 386 385 1 CURATED-SIMPLEX -17 37882882 37882882 C A sample_612-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_612-CURATED Normal UNPAIRED 184 0 184 0.0 98 98 0 171 171 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_613-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_613-CURATED Normal UNPAIRED 304 0 304 0.0 163 163 0 272 272 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_614-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_614-CURATED Normal UNPAIRED 175 0 175 0.0 106 106 0 164 164 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_615-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_615-CURATED Normal UNPAIRED 497 0 499 0.0 270 268 0 467 465 0 CURATED-SIMPLEX -17 37882882 37882882 C A sample_616-CURATED ERBB2 mskcc.org GRCh37 17 37882882 37882882 + Silent SNP C A sample_616-CURATED Normal UNPAIRED 460 0 460 0.0 247 247 0 424 424 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_893-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_893-CURATED Normal UNPAIRED 277 20 331 0.060423 172 137 20 310 257 20 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_894-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_894-CURATED Normal UNPAIRED 331 0 374 0.0 185 164 0 341 301 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_895-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_895-CURATED Normal UNPAIRED 415 42 512 0.0820312 254 206 26 477 384 41 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_896-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_896-CURATED Normal UNPAIRED 712 2 826 0.00242131 411 366 2 758 657 2 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_897-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_897-CURATED Normal UNPAIRED 230 19 274 0.0693431 142 114 17 262 218 19 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_898-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_898-CURATED Normal UNPAIRED 237 0 272 0.0 121 102 0 251 220 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_899-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_899-CURATED Normal UNPAIRED 268 16 309 0.0517799 154 132 8 277 238 14 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_900-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_900-CURATED Normal UNPAIRED 153 47 208 0.225962 113 80 27 197 142 45 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_901-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_901-CURATED Normal UNPAIRED 678 0 770 0.0 372 334 0 699 620 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_902-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_902-CURATED Normal UNPAIRED 411 0 449 0.0 199 181 0 409 376 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_903-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_903-CURATED Normal UNPAIRED 644 0 748 0.0 351 313 0 675 582 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_904-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_904-CURATED Normal UNPAIRED 362 6 472 0.0127119 261 186 5 446 342 5 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_905-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_905-CURATED Normal UNPAIRED 236 0 394 0.0 177 102 0 367 221 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_906-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_906-CURATED Normal UNPAIRED 488 0 547 0.0 279 250 0 523 467 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_907-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_907-CURATED Normal UNPAIRED 67 0 122 0.0 53 31 0 115 65 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_908-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_908-CURATED Normal UNPAIRED 404 2 462 0.004329 234 198 2 415 367 2 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_909-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_909-CURATED Normal UNPAIRED 326 0 354 0.0 159 150 0 325 298 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_910-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_910-CURATED Normal UNPAIRED 362 0 409 0.0 205 183 0 378 334 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_911-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_911-CURATED Normal UNPAIRED 346 0 395 0.0 195 171 0 364 317 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_912-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_912-CURATED Normal UNPAIRED 385 40 479 0.08350729999999999 249 190 32 434 346 34 CURATED-SIMPLEX -18 48584855 48584855 A TTT n_sample-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT n_sample-CURATED Normal UNPAIRED 374 2 435 0.0045977 208 179 0 406 347 2 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_913-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_913-CURATED Normal UNPAIRED 163 14 189 0.0740741 101 88 6 165 141 12 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_914-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_914-CURATED Normal UNPAIRED 438 1 526 0.00190114 258 207 1 484 404 1 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_915-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_915-CURATED Normal UNPAIRED 253 0 290 0.0 139 126 0 272 238 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_916-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_916-CURATED Normal UNPAIRED 285 22 351 0.0626781 194 155 13 328 267 19 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_917-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_917-CURATED Normal UNPAIRED 283 1 363 0.00275482 187 129 0 327 253 1 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_918-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_918-CURATED Normal UNPAIRED 190 0 218 0.0 107 95 0 201 176 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_919-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_919-CURATED Normal UNPAIRED 321 0 362 0.0 151 136 0 325 285 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_920-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_920-CURATED Normal UNPAIRED 162 9 183 0.0491803 99 86 6 165 144 9 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_921-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_921-CURATED Normal UNPAIRED 195 0 264 0.0 117 90 0 247 182 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_922-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_922-CURATED Normal UNPAIRED 149 0 164 0.0 84 76 0 158 144 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_923-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_923-CURATED Normal UNPAIRED 348 0 431 0.0 215 173 0 405 330 0 CURATED-SIMPLEX -18 48584855 48584855 A TTT sample_924-CURATED SMAD4 mskcc.org GRCh37 18 48584855 48584855 + Intron INS A TTT sample_924-CURATED Normal UNPAIRED 315 0 361 0.0 172 151 0 333 294 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1201-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1201-CURATED Normal UNPAIRED 314 2 334 0.00598802 140 121 1 312 292 2 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1202-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1202-CURATED Normal UNPAIRED 334 1 346 0.00289017 158 148 0 319 309 1 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1203-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1203-CURATED Normal UNPAIRED 463 1 492 0.00203252 212 185 0 462 435 1 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1204-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1204-CURATED Normal UNPAIRED 782 0 797 0.0 355 342 0 738 725 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1205-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1205-CURATED Normal UNPAIRED 271 1 288 0.00347222 130 115 0 274 257 1 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1206-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1206-CURATED Normal UNPAIRED 233 0 249 0.0 108 92 0 231 216 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1207-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1207-CURATED Normal UNPAIRED 259 0 269 0.0 117 108 0 253 243 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1208-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1208-CURATED Normal UNPAIRED 178 2 195 0.0102564 89 75 0 183 166 2 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1209-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1209-CURATED Normal UNPAIRED 683 0 729 0.0 294 248 0 683 638 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1210-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1210-CURATED Normal UNPAIRED 394 0 406 0.0 160 148 0 385 373 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1211-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1211-CURATED Normal UNPAIRED 672 1 693 0.001443 299 281 0 645 625 1 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1212-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1212-CURATED Normal UNPAIRED 430 3 447 0.00671141 226 212 0 427 412 3 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1213-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1213-CURATED Normal UNPAIRED 353 0 364 0.0 161 150 0 354 343 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1214-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1214-CURATED Normal UNPAIRED 472 0 516 0.0 236 194 0 496 452 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1215-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1215-CURATED Normal UNPAIRED 127 0 132 0.0 60 56 0 127 122 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1216-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1216-CURATED Normal UNPAIRED 372 3 406 0.00738916 169 141 1 370 339 2 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1217-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1217-CURATED Normal UNPAIRED 331 0 338 0.0 146 139 0 314 307 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1218-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1218-CURATED Normal UNPAIRED 378 0 398 0.0 184 167 0 374 354 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1219-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1219-CURATED Normal UNPAIRED 344 0 352 0.0 152 145 0 336 328 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1220-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1220-CURATED Normal UNPAIRED 427 1 447 0.00223714 191 172 1 415 395 0 CURATED-SIMPLEX -18 48584872 48584872 G T n_sample-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T n_sample-CURATED Normal UNPAIRED 376 0 401 0.0 177 153 0 383 359 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1221-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1221-CURATED Normal UNPAIRED 180 0 183 0.0 87 84 0 171 168 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1222-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1222-CURATED Normal UNPAIRED 456 0 498 0.0 216 175 0 469 428 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1223-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1223-CURATED Normal UNPAIRED 242 0 257 0.0 115 100 0 243 228 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1224-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1224-CURATED Normal UNPAIRED 313 3 330 0.00909091 156 142 1 316 299 3 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1225-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1225-CURATED Normal UNPAIRED 283 2 327 0.00611621 128 92 0 307 266 2 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1226-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1226-CURATED Normal UNPAIRED 195 0 198 0.0 90 87 0 188 185 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1227-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1227-CURATED Normal UNPAIRED 315 0 321 0.0 123 118 0 295 290 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1228-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1228-CURATED Normal UNPAIRED 172 1 176 0.00568182 84 81 0 163 159 1 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1229-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1229-CURATED Normal UNPAIRED 228 2 245 0.00816326 108 95 0 230 213 2 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1230-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1230-CURATED Normal UNPAIRED 149 0 155 0.0 81 75 0 149 143 0 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1231-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1231-CURATED Normal UNPAIRED 364 1 402 0.00248756 177 143 0 384 346 1 CURATED-SIMPLEX -18 48584872 48584872 G T sample_1232-CURATED SMAD4 mskcc.org GRCh37 18 48584872 48584872 + Intron SNP G T sample_1232-CURATED Normal UNPAIRED 330 1 342 0.00292398 158 149 0 323 311 1 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1509-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1509-CURATED Normal UNPAIRED 423 0 424 0.0 250 249 0 386 385 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1510-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1510-CURATED Normal UNPAIRED 388 0 389 0.0 259 258 0 349 348 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1511-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1511-CURATED Normal UNPAIRED 602 0 603 0.0 373 372 0 528 527 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1512-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1512-CURATED Normal UNPAIRED 783 0 787 0.0 489 487 0 711 707 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1513-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1513-CURATED Normal UNPAIRED 398 0 398 0.0 239 239 0 357 357 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1514-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1514-CURATED Normal UNPAIRED 305 0 306 0.0 194 193 0 272 271 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1515-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1515-CURATED Normal UNPAIRED 426 0 426 0.0 272 272 0 374 374 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1516-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1516-CURATED Normal UNPAIRED 289 0 289 0.0 177 177 0 264 264 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1517-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1517-CURATED Normal UNPAIRED 789 0 792 0.0 543 542 0 701 698 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1518-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1518-CURATED Normal UNPAIRED 456 0 456 0.0 311 311 0 420 420 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1519-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1519-CURATED Normal UNPAIRED 736 0 738 0.0 482 480 0 643 641 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1520-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1520-CURATED Normal UNPAIRED 534 0 534 0.0 337 337 0 475 475 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1521-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1521-CURATED Normal UNPAIRED 498 0 499 0.0 345 344 0 461 460 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1522-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1522-CURATED Normal UNPAIRED 637 0 638 0.0 395 395 0 580 579 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1523-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1523-CURATED Normal UNPAIRED 109 0 109 0.0 66 66 0 100 100 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1524-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1524-CURATED Normal UNPAIRED 541 0 545 0.0 339 336 0 457 453 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1525-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1525-CURATED Normal UNPAIRED 359 0 359 0.0 238 238 0 316 316 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1526-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1526-CURATED Normal UNPAIRED 521 0 522 0.0 325 325 0 466 465 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1527-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1527-CURATED Normal UNPAIRED 570 0 570 0.0 410 410 0 520 520 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1528-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1528-CURATED Normal UNPAIRED 569 0 572 0.0 357 355 0 514 511 0 CURATED-SIMPLEX -18 48586244 48586244 C T n_sample-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T n_sample-CURATED Normal UNPAIRED 505 0 511 0.0 302 301 0 453 448 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1529-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1529-CURATED Normal UNPAIRED 228 0 228 0.0 146 146 0 200 200 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1530-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1530-CURATED Normal UNPAIRED 579 0 583 0.0 366 363 0 531 527 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1531-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1531-CURATED Normal UNPAIRED 401 0 405 0.0 256 254 0 362 360 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1532-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1532-CURATED Normal UNPAIRED 471 0 471 0.0 318 318 0 424 424 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1533-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1533-CURATED Normal UNPAIRED 452 0 456 0.0 283 280 0 393 390 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1534-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1534-CURATED Normal UNPAIRED 259 1 261 0.00383142 163 161 1 229 227 1 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1535-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1535-CURATED Normal UNPAIRED 437 0 437 0.0 265 265 0 381 381 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1536-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1536-CURATED Normal UNPAIRED 206 0 206 0.0 128 128 0 182 182 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1537-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1537-CURATED Normal UNPAIRED 365 0 366 0.0 217 217 0 320 319 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1538-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1538-CURATED Normal UNPAIRED 181 0 182 0.0 128 127 0 169 168 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1539-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1539-CURATED Normal UNPAIRED 500 0 503 0.0 330 330 0 459 457 0 CURATED-SIMPLEX -18 48586244 48586244 C T sample_1540-CURATED SMAD4 mskcc.org GRCh37 18 48586244 48586244 + Missense_Mutation SNP C T sample_1540-CURATED Normal UNPAIRED 559 0 559 0.0 358 358 0 511 511 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1817-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1817-CURATED Normal UNPAIRED 189 1 214 0.0046729 153 152 0 204 184 1 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1818-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1818-CURATED Normal UNPAIRED 216 5 246 0.0203252 160 158 0 234 209 4 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1819-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1819-CURATED Normal UNPAIRED 312 1 338 0.00295858 222 218 0 318 296 1 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1820-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1820-CURATED Normal UNPAIRED 419 3 467 0.00642398 288 281 0 445 403 3 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1821-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1821-CURATED Normal UNPAIRED 134 0 150 0.0 100 98 0 147 133 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1822-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1822-CURATED Normal UNPAIRED 182 0 193 0.0 126 125 0 178 169 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1823-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1823-CURATED Normal UNPAIRED 178 0 192 0.0 120 120 0 178 170 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1824-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1824-CURATED Normal UNPAIRED 143 0 150 0.0 111 111 0 140 135 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1825-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1825-CURATED Normal UNPAIRED 463 11 520 0.0211538 326 322 0 496 443 10 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1826-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1826-CURATED Normal UNPAIRED 176 1 184 0.00543478 137 137 0 178 171 1 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1827-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1827-CURATED Normal UNPAIRED 399 6 446 0.0134529 261 261 0 415 376 4 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1828-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1828-CURATED Normal UNPAIRED 273 1 319 0.0031348 201 199 0 311 267 1 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1829-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1829-CURATED Normal UNPAIRED 191 0 203 0.0 130 129 0 193 182 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1830-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1830-CURATED Normal UNPAIRED 303 7 343 0.0204082 238 232 0 334 297 7 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1831-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1831-CURATED Normal UNPAIRED 92 1 95 0.0105263 53 53 0 88 85 1 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1832-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1832-CURATED Normal UNPAIRED 219 1 251 0.00398406 179 174 0 242 214 1 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1833-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1833-CURATED Normal UNPAIRED 188 0 193 0.0 113 113 0 178 174 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1834-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1834-CURATED Normal UNPAIRED 243 7 281 0.024911000000000003 190 188 0 267 234 6 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1835-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1835-CURATED Normal UNPAIRED 207 1 224 0.00446429 156 154 0 214 198 1 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1836-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1836-CURATED Normal UNPAIRED 239 7 277 0.0252708 203 203 0 265 233 7 CURATED-SIMPLEX -18 57571783 57571783 T - n_sample-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - n_sample-CURATED Normal UNPAIRED 266 3 301 0.00996678 210 207 0 289 257 3 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1837-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1837-CURATED Normal UNPAIRED 119 0 127 0.0 83 83 0 124 116 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1838-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1838-CURATED Normal UNPAIRED 278 2 315 0.00634921 210 207 0 305 272 1 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1839-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1839-CURATED Normal UNPAIRED 201 0 214 0.0 148 147 0 202 191 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1840-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1840-CURATED Normal UNPAIRED 211 1 231 0.004329 137 136 0 225 205 1 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1841-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1841-CURATED Normal UNPAIRED 157 1 177 0.00564972 113 111 0 172 153 1 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1842-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1842-CURATED Normal UNPAIRED 128 1 141 0.0070922 84 84 0 134 122 1 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1843-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1843-CURATED Normal UNPAIRED 189 2 217 0.00921659 155 153 0 211 184 2 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1844-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1844-CURATED Normal UNPAIRED 94 0 99 0.0 63 63 0 97 92 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1845-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1845-CURATED Normal UNPAIRED 176 0 184 0.0 129 129 0 176 169 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1846-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1846-CURATED Normal UNPAIRED 112 0 120 0.0 83 80 0 118 110 0 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1847-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1847-CURATED Normal UNPAIRED 199 2 239 0.008368200000000001 165 162 0 238 199 2 CURATED-SIMPLEX -18 57571783 57571783 T - sample_1848-CURATED PMAIP1 mskcc.org GRCh37 18 57571783 57571783 + 3'Flank DEL T - sample_1848-CURATED Normal UNPAIRED 174 1 187 0.00534759 132 131 0 179 169 1 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2125-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2125-CURATED Normal UNPAIRED 188 6 215 0.027907 153 153 0 204 183 5 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2126-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2126-CURATED Normal UNPAIRED 214 2 245 0.00816326 160 160 0 232 206 1 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2127-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2127-CURATED Normal UNPAIRED 295 6 338 0.0177515 222 221 0 318 286 5 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2128-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2128-CURATED Normal UNPAIRED 405 6 467 0.012847999999999998 288 287 0 445 393 4 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2129-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2129-CURATED Normal UNPAIRED 119 3 150 0.02 100 100 0 147 118 3 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2130-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2130-CURATED Normal UNPAIRED 175 0 193 0.0 126 126 0 178 164 0 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2131-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2131-CURATED Normal UNPAIRED 162 3 192 0.015625 120 120 0 178 158 2 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2132-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2132-CURATED Normal UNPAIRED 133 0 150 0.0 111 111 0 140 129 0 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2133-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2133-CURATED Normal UNPAIRED 421 24 519 0.046242800000000014 326 322 0 495 411 16 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2134-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2134-CURATED Normal UNPAIRED 163 3 184 0.0163043 137 137 0 178 161 2 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2135-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2135-CURATED Normal UNPAIRED 383 5 446 0.011210799999999998 261 261 0 415 365 4 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2136-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2136-CURATED Normal UNPAIRED 263 0 317 0.0 200 199 0 310 260 0 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2137-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2137-CURATED Normal UNPAIRED 176 7 203 0.0344828 130 128 0 193 170 6 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2138-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2138-CURATED Normal UNPAIRED 297 3 343 0.00874636 238 236 0 334 294 2 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2139-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2139-CURATED Normal UNPAIRED 84 3 95 0.0315789 53 53 0 88 79 1 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2140-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2140-CURATED Normal UNPAIRED 223 1 251 0.00398406 179 175 0 242 219 1 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2141-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2141-CURATED Normal UNPAIRED 179 3 192 0.015625 113 113 0 177 168 2 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2142-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2142-CURATED Normal UNPAIRED 242 4 281 0.014234899999999997 190 189 0 267 234 4 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2143-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2143-CURATED Normal UNPAIRED 184 5 225 0.0222222 156 156 0 214 180 3 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2144-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2144-CURATED Normal UNPAIRED 237 3 278 0.0107914 203 201 0 265 231 3 CURATED-SIMPLEX -18 57571784 57571784 C - n_sample-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - n_sample-CURATED Normal UNPAIRED 257 5 302 0.0165563 210 209 0 290 250 3 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2145-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2145-CURATED Normal UNPAIRED 112 0 127 0.0 83 82 0 124 111 0 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2146-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2146-CURATED Normal UNPAIRED 286 3 314 0.00955414 210 210 0 304 280 2 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2147-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2147-CURATED Normal UNPAIRED 191 3 214 0.014018700000000002 148 148 0 202 185 2 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2148-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2148-CURATED Normal UNPAIRED 197 2 231 0.00865801 137 137 0 224 193 1 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2149-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2149-CURATED Normal UNPAIRED 149 4 175 0.0228571 113 111 0 170 146 3 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2150-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2150-CURATED Normal UNPAIRED 121 5 142 0.035211300000000015 84 83 0 135 117 4 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2151-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2151-CURATED Normal UNPAIRED 189 2 216 0.00925926 154 153 0 210 186 1 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2152-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2152-CURATED Normal UNPAIRED 85 3 99 0.030303 63 63 0 97 83 2 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2153-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2153-CURATED Normal UNPAIRED 156 1 184 0.00543478 129 129 0 176 154 1 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2154-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2154-CURATED Normal UNPAIRED 99 5 120 0.0416667 83 82 0 118 97 4 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2155-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2155-CURATED Normal UNPAIRED 206 2 239 0.008368200000000001 165 165 0 238 205 2 CURATED-SIMPLEX -18 57571784 57571784 C - sample_2156-CURATED PMAIP1 mskcc.org GRCh37 18 57571784 57571784 + 3'Flank DEL C - sample_2156-CURATED Normal UNPAIRED 165 4 187 0.021390400000000004 132 132 0 179 164 3 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2433-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2433-CURATED Normal UNPAIRED 432 0 468 0.0 189 153 0 434 413 0 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2434-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2434-CURATED Normal UNPAIRED 365 2 390 0.00512821 161 136 2 357 344 1 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2435-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2435-CURATED Normal UNPAIRED 545 2 604 0.00331126 267 208 2 554 516 1 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2436-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2436-CURATED Normal UNPAIRED 683 4 759 0.00527009 333 257 4 684 644 0 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2437-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2437-CURATED Normal UNPAIRED 361 8 399 0.0200501 142 104 8 372 346 5 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2438-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2438-CURATED Normal UNPAIRED 306 0 328 0.0 130 108 0 298 286 0 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2439-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2439-CURATED Normal UNPAIRED 354 8 414 0.0193237 181 121 8 348 318 1 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2440-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2440-CURATED Normal UNPAIRED 252 2 282 0.0070922 123 93 2 261 240 2 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2441-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2441-CURATED Normal UNPAIRED 738 7 793 0.00882724 338 283 7 716 685 4 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2442-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2442-CURATED Normal UNPAIRED 423 7 492 0.014227600000000003 204 135 7 449 406 2 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2443-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2443-CURATED Normal UNPAIRED 770 2 825 0.00242424 358 303 2 739 713 1 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2444-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2444-CURATED Normal UNPAIRED 508 5 550 0.00909091 223 182 5 509 483 3 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2445-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2445-CURATED Normal UNPAIRED 423 9 484 0.018595 176 115 9 445 405 2 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2446-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2446-CURATED Normal UNPAIRED 577 3 634 0.00473186 260 204 3 584 550 1 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2447-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2447-CURATED Normal UNPAIRED 150 3 179 0.0167598 86 57 3 158 140 1 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2448-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2448-CURATED Normal UNPAIRED 576 2 592 0.00337838 169 154 2 551 546 0 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2449-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2449-CURATED Normal UNPAIRED 314 14 356 0.0393258 154 112 14 313 286 4 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2450-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2450-CURATED Normal UNPAIRED 533 2 560 0.00357143 205 179 2 532 515 1 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2451-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2451-CURATED Normal UNPAIRED 400 6 450 0.0133333 178 128 6 405 379 6 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2452-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2452-CURATED Normal UNPAIRED 549 2 600 0.00333333 247 196 2 554 518 0 CURATED-SIMPLEX -19 10273379 10273379 A T n_sample-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T n_sample-CURATED Normal UNPAIRED 433 0 464 0.0 201 171 0 434 411 0 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2453-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2453-CURATED Normal UNPAIRED 243 5 294 0.0170068 149 98 5 248 214 4 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2454-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2454-CURATED Normal UNPAIRED 684 3 737 0.00407056 251 199 3 682 653 1 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2455-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2455-CURATED Normal UNPAIRED 355 4 392 0.0102041 195 158 4 354 330 3 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2456-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2456-CURATED Normal UNPAIRED 414 4 448 0.00892857 167 133 4 413 395 0 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2457-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2457-CURATED Normal UNPAIRED 627 0 651 0.0 222 198 0 610 603 0 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2458-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2458-CURATED Normal UNPAIRED 239 3 262 0.0114504 105 83 3 237 222 2 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2459-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2459-CURATED Normal UNPAIRED 418 9 468 0.0192308 197 147 9 413 385 2 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2460-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2460-CURATED Normal UNPAIRED 201 7 250 0.028 115 66 7 214 189 4 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2461-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2461-CURATED Normal UNPAIRED 296 3 322 0.00931677 145 119 3 287 271 0 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2462-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2462-CURATED Normal UNPAIRED 159 1 174 0.00574713 74 59 1 164 153 0 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2463-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2463-CURATED Normal UNPAIRED 574 1 603 0.00165837 204 176 1 574 557 1 CURATED-SIMPLEX -19 10273379 10273379 A T sample_2464-CURATED DNMT1 mskcc.org GRCh37 19 10273379 10273379 + Missense_Mutation SNP A T sample_2464-CURATED Normal UNPAIRED 380 4 414 0.00966184 175 141 4 383 360 1 CURATED-SIMPLEX diff --git a/tests/test_genotype_variants.py b/tests/test_genotype_variants.py index 2f20fde..e132bfc 100644 --- a/tests/test_genotype_variants.py +++ b/tests/test_genotype_variants.py @@ -7,16 +7,18 @@ import pandas as pd from genotype_variants.commands import small_variants - +from genotype_variants.create_duplex_simplex_dataframe import ( + create_duplex_simplex_dataframe as cdsd, +) class TestGenotype_variants(unittest.TestCase): """Tests for `genotype_variants` package.""" def setUp(self): """Set up test fixtures, if any.""" - self.mutation_key = ['Chromosome', 'Start_Position', 'End_Position', 'Reference_Allele', 'Tumor_Seq_Allele1'] - self.d_maf = pd.read_csv('tests/test_data/test_duplex.maf', sep="\t", header="infer") - self.s_maf = pd.read_csv('tests/test_data/test_simplex.maf', sep="\t", header="infer") + self.mutation_key = ['Chromosome', 'Start_Position', 'End_Position', 'Reference_Allele', 'Tumor_Seq_Allele2'] + self.d_maf = pd.read_csv('tests/test_data/C-100000-L002-d02-DUPLEX_genotyped.maf', sep="\t", header="infer") + self.s_maf = pd.read_csv('tests/test_data/C-100000-L002-d02-SIMPLEX_genotyped.maf', sep="\t", header="infer") self.d_maf = self.d_maf.set_index(self.mutation_key, drop=False) self.s_maf = self.s_maf.set_index(self.mutation_key, drop=False) @@ -41,26 +43,25 @@ def test_merge_simplex_duplex(self): :return: """ - df_merge = small_variants.create_duplex_simplex_dataframe(self.s_maf, self.d_maf) + df_merge = cdsd(self.s_maf, self.d_maf) df_merge = df_merge.sort_index() - expected = pd.read_csv('tests/test_data/expected.maf', sep='\t') + expected = pd.read_csv('tests/test_data/C-100000-L002-d02-SIMPLEX-DUPLEX_genotyped.maf', sep='\t') expected = expected.set_index(self.mutation_key, drop=False) expected = expected.sort_index() - pd.testing.assert_frame_equal(df_merge, expected) # SNP - snp_index = (1, 8080157, 8080157, 'T', 'A') - assert df_merge.loc[snp_index]['t_ref_count_fragment'] == 1549 - assert df_merge.loc[snp_index]['t_alt_count_fragment'] == 1 - assert df_merge.loc[snp_index]['t_total_count_fragment'] == 1550 - # INS - insertion_index = (18, 48584855, 48584855, 'A', 'TTT') - assert df_merge.loc[insertion_index]['t_ref_count_fragment'] == 694 - assert df_merge.loc[insertion_index]['t_alt_count_fragment'] == 4 - assert df_merge.loc[insertion_index]['t_total_count_fragment'] == 698 + snp_index = (16, 68842732, 68842732, 'A', 'C') + assert df_merge.loc[snp_index]['t_ref_count_fragment_simplex_duplex'] == 2737 + assert df_merge.loc[snp_index]['t_alt_count_fragment_simplex_duplex'] == 3 + assert df_merge.loc[snp_index]['t_total_count_fragment_simplex_duplex'] == 2740 + # # INS + # insertion_index = (18, 48584855, 48584855, 'A', 'TTT') + # assert df_merge.loc[insertion_index]['t_ref_count_fragment'] == 694 + # assert df_merge.loc[insertion_index]['t_alt_count_fragment'] == 4 + # assert df_merge.loc[insertion_index]['t_total_count_fragment'] == 698 # DEL - deletion_index = (18, 57571783, 57571783, 'T', '-') - assert df_merge.loc[deletion_index]['t_ref_count_fragment'] == 514 - assert df_merge.loc[deletion_index]['t_alt_count_fragment'] == 6 - assert df_merge.loc[deletion_index]['t_total_count_fragment'] == 520 + deletion_index = (5, 1295253, 1295262, 'GGGTCGGGAC', '-') + assert df_merge.loc[deletion_index]['t_ref_count_fragment_simplex_duplex'] == 537 + assert df_merge.loc[deletion_index]['t_alt_count_fragment_simplex_duplex'] == 0 + assert df_merge.loc[deletion_index]['t_total_count_fragment_simplex_duplex'] == 537