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Old 05-31-2012, 01:54 PM   #2
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Join Date: Jan 2010
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Originally Posted by NGSNewbie1 View Post
Sorry for this newbie question but I haven't been able to get an answer after searching around. Is there a program that automagically produces the somatic mutations from inputted tumor and normal VCF files? I'm trying to avoid using a tool like SomaticSniper with BAM files because of size/computation etc. If I have the VCF files, is there an easy way to just select the differences?

Thank you in advance for any guidance!
The thing is that these tools like SomaticSniper are designed to work on the bam files for a reason. Whilst a subtractive approach with VCFs will work for some somatic calls, most genotypers aren't really geared up for variant detection in heterogenous cancer samples.

NGS is not always speedy work, sometimes it's better just to use the tools than take the shortcuts
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