Dear professor,
Thanks a lot for such a powerful tool.
When I check Allele Frequency (AF), found AF != VD/DP, see example like this:
chr7 55236793 . TTTC T 83 PASS SAMPLE=S1;TYPE=Deletion;DP=436;VD=6;AF=0.0133;BIAS=2:2;REFBIAS=270:169;VARBIAS=1:5;PMEAN=25.7;PSTD=1;QUAL=32.2;QSTD=1;SBF=0.03599;ODDRATIO=7.95226;MQ=60;SN=12;HIAF=0.0149;ADJAF=0;SHIFT3=2;MSI=13;MSILEN=1;NM=3.8;HICNT=6;HICOV=402;LSEQ=GAACCCTGGAGGAATAGCTA;RSEQ=TTTTTTTTTTTTGTCGAGAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:436:6:439,6:0.0133:270,169:1,5
In which , AF = VD/DP = 6/436 = 0.01376
or something I'm wrong?
Dear professor, Thanks a lot for such a powerful tool. When I check Allele Frequency (AF), found AF != VD/DP, see example like this: chr7 55236793 . TTTC T 83 PASS SAMPLE=S1;TYPE=Deletion;DP=436;VD=6;AF=0.0133;BIAS=2:2;REFBIAS=270:169;VARBIAS=1:5;PMEAN=25.7;PSTD=1;QUAL=32.2;QSTD=1;SBF=0.03599;ODDRATIO=7.95226;MQ=60;SN=12;HIAF=0.0149;ADJAF=0;SHIFT3=2;MSI=13;MSILEN=1;NM=3.8;HICNT=6;HICOV=402;LSEQ=GAACCCTGGAGGAATAGCTA;RSEQ=TTTTTTTTTTTTGTCGAGAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:436:6:439,6:0.0133:270,169:1,5
In which , AF = VD/DP = 6/436 = 0.01376 or something I'm wrong?
look forward to your reply !