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?