Feature/docker

.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 }}

.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

.gitignore

@@ -104,3 +104,4 @@ ENV/
 # IDE settings
 .vscode/
 .idea/
+tests/.DS_Store

.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

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

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
 -----

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:

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

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

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 = [ ]
 
@@ -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',

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

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

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

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