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Old 09-10-2014, 10:12 AM   #7
lethalfang
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Location: San Francisco, CA

Join Date: Aug 2011
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Quote:
Originally Posted by vd4mindia View Post
@lethalfang
`Would you like to share the pipeline for finding somatic mutations. I have 2 samples, one low and one high grade tumor and its normal. I want to detect the point somatic mutations. I have already employed GATK, VarScan and Mutect, but I have some descrepancy when am looking at my Low grade tumor since it is 50% pure. So I would like to try something more and have a read statistics like you have shown to validate the hits. If its ok for you
That's something I used to do a couple of years ago.
I just had a script to get those information out of the Strelka output vcf file. I had all those Strelka out directories in a single location, and ran this script to "summarize" all mutation calls from all the samples:

http://kimlab.surgery.ucsf.edu/media...a_findings.txt

It also calls annovar, which has a hard-coded path within the script.
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