Question: Problem understanding GT from Varscan's vcf output
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gravatar for ww22runner
4 months ago by
ww22runner0
ww22runner0 wrote:

Hello all,

I am trying to look for somatic variants in paired tumor/normal samples and have been using Varscan's somatic and processSomatic commands to obtain a vcf. However, I am having trouble understanding the output.

For somatic variants called with high confidence, an example is:

> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NORMAL  TUMOR 
>chr10   42400631        .       C       T       .      PASS    DP=41;SOMATIC;SS=2;SSC=14;GPV=1E0;SPV=3.2237E-2    GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:26:24:2:7.69%:12,12,2,0   0/1:.:15:10:5:33.33%:9,1,3,2

In this example, when I look at the normal sample, the DP value is 26 out of which 24 match the reference allele while 2 do not and thus the allele frequency of 7.69%. According to my understanding, Varscan's default parameter for min-freq-for-hom is 0.75 meaning if in this case the reference allele occurs in (100-7.69)% = 92.31% > 75%, the GT for normal sample should be 0/0 instead of 1/1?

If anyone could kindly help me understand such vcf outputs, I would greatly appreciate it.

Also, could anyone tell me how processSomatic command separates certain somatic variant calls as high confidence and what conditions it uses to do this?

Thank you

varscan • 233 views
ADD COMMENTlink modified 4 months ago by RamRS20k • written 4 months ago by ww22runner0
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