search

hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
311 stars 116 forks source link

How to use speedseq somatic #57

Closed bioxu closed 8 years ago

bioxu commented 8 years ago

Hi,all I am beginer with SpeedSeq.I have 40 cancer-normal WGS and want to call somatic snps,but I don't konw how to use speedseq somatic exactly. 1.How to create a tumor or normal bam file from 40 WGS data,respectively. 2.GRCh37 is the necessary genome reference fasta file? Can I use h19?

@cc2qe expect your reply.

cc2qe commented 8 years ago

here is an example workflow for each tumor normal pair: https://github.com/hall-lab/speedseq#call-variants-on-a-tumornormal-pair

It's better to use GRCh37 than hg19, because some of the downstream steps (CNVnator for structural variation detection) cannot handle chromosome prefixes

bioxu commented 8 years ago

Dear cc2qe, Thanks for your reply. you know I'm a beginer to call somatic snp,so I have these question:

  1. Should I call somatic snp for each tumor normal pair use speedseq-somatic?If yes, what should I do to integrate these somatic files?(I have 40 samples)
  2. If I completely call somatic,annotation is next work,I had used Annovar,I want to know if I can use this tool to substitute the VEP? Thanks.