Comparing VCFs for somatic mutations?

More Navonil De Sarkar's questions See All

Is there a tool?

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Can anyone provide a *.bed file human exome?

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Can you suggest a P-value cutoff for a somatic variant call?

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Is there any restriction enzyme which can specifically cut a DNA strand sensing either a stretch of 8Cs or 8Gs?

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Navonil De Sarkar

"So, I am looking for somatic mutation at first, between normal sample and cancer sample VCFs. Now, some tools like Varscan can compare the respective pileups,and find out somatic mutations as well as LOH sites, All I am looking for is some tool, which can perform the same with respective VCFs as input. But ya, as you said, finally I will try to see commonality of all those somatic sites, all across my sample pairs.

Poornima Nagaraj

SomaticSniper is a tool to find somatic mutation from paired VCFs .

You can also try with Strelka which proves to be more accurate .

The paper which cites that is :http://www.ncbi.nlm.nih.gov/pubmed/22581179