Question: Identify Germline Mutations
gravatar for yliuboston
6.6 years ago by
yliuboston20 wrote:

Hi everyone,

I am now trying to identify germline mutations from tumor and matched normal samples in TCGA and also I need to know this germline mutation occur in exactly which samples. I know some software like VarScan can do this, but they are all working on .bam file, I only have some .vcf files, any software or protocol can do the following? 1. Identify germline mutation in a group of tumor and matched normal. 2. For each of germline mutations identified, tell which sample they call.

Thanks in advance!

ADD COMMENTlink modified 6.6 years ago by Charles Warden7.9k • written 6.6 years ago by yliuboston20
gravatar for Charles Warden
6.6 years ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

1) VarScan actually uses .pileup (it doesn't directly read .bam file)

2) If you already have a list of variants in a .vcf file, I don't really think you can call somatic mutations by doing anything beyond comparing overlap between two files (which is something I would do using a custom Perl script). If at all possible, I would try to find a more raw form of data and use standard tools like VarScan, MuTect, SomaticSniper, etc.

ADD COMMENTlink written 6.6 years ago by Charles Warden7.9k

It smells like a homework problem. He has two vcf and just needs to subtract.

ADD REPLYlink written 6.6 years ago by karl.stamm3.8k

Thanks a lot for your explanation. I think I have a .vcf file that have compared one tumor and its matched normal, so I guess the "subtraction" job has been done. But I am not quite sure among all those variants called, which germline mutations that I should be confirmed to use in the following analysis, like filter=pass, or based on DP bigger than a threshold? If I donot have access to a more raw form of data, is there a standard way to do this? Thanks in advance!

ADD REPLYlink written 6.6 years ago by yliuboston20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1876 users visited in the last hour