Here is an example of the sequencing output. As was suggested, I should filter the variants based on the bam readcounts (or read depth or allelic depth?). I'm confused of the definition and the discrimination among these three terms. Is the bam readcounts the same as AD or DP? Can anyone tell me the difference and which one should I use to filter the variants? Thanks.
FORMAT TUMOR GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP 0/1:196,25:0.049:221:73,8:123,17:0.111,0.010,0.113:2.631e-06,0.998,1.645e-03