From 3fc46177f00ffe7ec7fd65f10f2fa5f0f63f0726 Mon Sep 17 00:00:00 2001 From: Colby Chiang Date: Sun, 29 Mar 2015 13:11:41 -0500 Subject: [PATCH] Update README.md formatting --- README.md | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index d9bb185..3f7b67c 100644 --- a/README.md +++ b/README.md @@ -375,7 +375,8 @@ tumor.bam tumor BAM file(s) (comma separated BAMs for multiple libraries speedseq var \ -o NA12878 \ -w annotations/ceph18.b37.include.2014-01-15.bed \ - human_g1k_v37.fasta NA12878.bam + human_g1k_v37.fasta \ + NA12878.bam ``` 3. Use `speedseq sv` to call structural variants. The optional `-g` and `-d` flags perform breakend genotyping and read-depth calculation respectively @@ -394,13 +395,19 @@ tumor.bam tumor BAM file(s) (comma separated BAMs for multiple libraries 1. Use `speedseq align` to produce a sorted, duplicate-marked, BAM alignment of each library. ``` speedseq align -o NA12878_S1 -R "@RG\tID:NA12878.S1\tSM:NA12878\tLB:lib1" \ - human_g1k_v37.fasta NA12878.S1.1.fq.gz NA12878.S1.2.fq.gz + human_g1k_v37.fasta \ + NA12878.S1.1.fq.gz \ + NA12878.S1.2.fq.gz speedseq align -o NA12878_S2 -R "@RG\tID:NA12878.S2\tSM:NA12878\tLB:lib2" \ - human_g1k_v37.fasta NA12878.S2.1.fq.gz NA12878.S2.2.fq.gz + human_g1k_v37.fasta \ + NA12878.S2.1.fq.gz \ + NA12878.S2.2.fq.gz speedseq align -o NA12878_S3 -R "@RG\tID:NA12878.S3\tSM:NA12878\tLB:lib3" \ - human_g1k_v37.fasta NA12878.S3.1.fq.gz NA12878.S3.2.fq.gz + human_g1k_v37.fasta \ + NA12878.S3.1.fq.gz \ + NA12878.S3.2.fq.gz ``` 2. Merge the samples @@ -459,7 +466,10 @@ tumor.bam tumor BAM file(s) (comma separated BAMs for multiple libraries speedseq var \ -o cephtrio \ -w annotations/ceph18.b37.include.2014-01-15.bed \ - human_g1k_v37.fasta NA12877.bam NA12878.bam NA12879.bam + human_g1k_v37.fasta \ + NA12877.bam \ + NA12878.bam \ + NA12879.bam ``` 3. Use `speedseq sv` to call structural variants on multiple samples.