Question: Is it possible to extract somatic variants from paired VCF files?
0
gravatar for csardas
2.1 years ago by
csardas0
csardas0 wrote:

Hi all,

I have 2 paired VCF files (normal and tumor sample). Is it possible to extract somatic variants from VCF directly? or I have to go back to bam files and run Mutect or VarScan?

somatic vcf • 798 views
ADD COMMENTlink modified 2.1 years ago by biomaster180 • written 2.1 years ago by csardas0

So essentially you would want to find variants which are present in the tumor.vcf and not in the normal.vcf?

ADD REPLYlink written 2.1 years ago by WouterDeCoster38k
0
gravatar for biomaster
2.1 years ago by
biomaster180
San Jose
biomaster180 wrote:

Yes, it is possible. Two ways:
1, the simple way, check the frequency for the mutations exist in both, if normal AF is close to 0.5 or 1.0, and tumor AF is more or less, then it is germline.
2, better way, but more complicated. Use the allele count and depth of the mutations exist in both, and then do a t-test, calculate the p-value.

ADD COMMENTlink written 2.1 years ago by biomaster180
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