Question: Exome-seq; Which tools to predict significantly muated genes .
gravatar for Chirag Nepal
23 months ago by
Chirag Nepal2.1k
Chirag Nepal2.1k wrote:

Hi there,

I analyzed some publicly available exome-seq data, and do not have matched normal/germline.

I identified somatic mutation (VCF format), by setting high filtering threshold. Which tool can be used to predict significantly mutated genes from these list ? Previously i used genome-music to find signifiacntly mutated genes, which requires both tumor/normal samples, and i dont't have matcher normal. Which tools cam predict significant mutations without matched normal samples.
Thanks !

cnv music varscan • 1.1k views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 23 months ago by Chirag Nepal2.1k

Maybe this post could help you. It is very tricky to find somatic mutations without the matched normal pairs. Taking in to account the "somatic" definition itself, how could you distinguish between somatic mutations from germline ones without a normal samples to make the comparison against?

Sorry for not being more helpful :)

ADD REPLYlink written 23 months ago by iraun3.4k

this is also my question, I found these posts but did not try yet. I read something about SKAT or burden test with 1000 genome as control

Somatic mutation calling without matched normal

Calling variants in blood tumor samples without matched normal samples

ADD REPLYlink modified 23 months ago • written 23 months ago by F3.1k
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