Changhan Yoon

I missed filtering steps which I made. It's my mistake.

Hi, I am confused. I am using VarScan2 (2.3.9) to identify and profile somatic mutations from cfDNAs and matched normal blood samples. When I used 0.005 for –-min-var-freq, I could not find some variants with higher VAF. However, when I used 0.05 for --min-var-freq, I found previously unfound variants with VAF over 0.05. For example, A variant (chr2 29606628 . C G . PASS DP=1775;SOMATIC;SS=2;SSC=255;GPV=1E0;SPV=1.136E-98; GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:447:444:0:0%:240,204,0,0 0/1:.:1328:700:601:46.2%:349,351,313,288)...

Hi, I am confused. I am using VarScan2 (2.3.9) to identify and profile somatic mutations from cfDNAs and matched normal blood samples. When I used 0.005 for –-min-var-freq, I could not find some variants with higher VAF. However, when I used 0.05 for --min-var-freq, I found previously unfound variants with VAF over 0.05. For example, A variant (chr2 29606628 . C G . PASS DP=1775;SOMATIC;SS=2;SSC=255;GPV=1E0;SPV=1.136E-98; GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:447:444:0:0%:240,204,0,0 0/1:.:1328:700:601:46.2%:349,351,313,288)...