Difference between read depth, allelic depth and bam readcounts

Question

[lincaijin1994]

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

[desouzareis.r]

Hi, usually the DP field is used to filter variants and also AF. Here there is good information about these fields Allele Depth (AD) is lower than expected VCF - Variant Call Format

"INFO" field DP - this includes all reads that overlap a variant after local realignment, which pass the quality filters.

"FORMAT" field DP - this includes only informative reads for that sample.

"FORMAT" field AD - this includes only informative reads for each allele. The sum of all AD = DP

Answer 1

[binodregmi30]

you should refer the read dept. If you refer allelic depth count, it may create inconsistency in single for biallelic site.