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DP is not reporting filtered read numbers
I am using GATK version 3.3 and ran haplotype caller with -mmq 30 and -mbq 20. The output of one of the positions in the VCF is below.
chr13 58264978 . C . . . GT:AD:DP:GQ:PL 0/0:22,1:23:54:0,54,655
I used IGV to validate this position. IGV reports, like GATK does that there are 23 total reads covering that position. Although, there are also 4 reads that have a phred score of less than 20 at the position above. The DP statistic seems to be recording the number of unfiltered reads, but not the filtered ones. Do you know why this is?