AD larger than DP?

[thelingxichen]

Hi,

When I check the vcf head infomation, I suppose DP > AD = SR + DR.

##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth of coverage: Number of reads covering site.">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele depth: Number of reads supporting the variant">

While I found some AD value is larger than DP in a normal-tumor pair. Is this a bug?

GT:AD:DP:GQ:PL:SR:DR:LR:LO      0/1:17:29:24.8:47.9,0,24.8:17:0:-48.36:48.36    1/1:31:28:8.4:92.4,8.4,0:31:0:-92.42:92.42

[walaj]

This is actually not a bug. This is because coverage is defined as a per-base coverage (at the breakpoint), but discordant reads can span across the breakpoint. As the insert size gets very large (e.g. a mate-pair library), the counts of DR should be >> DP. Also, AD != SR + DR because a read could be both spit and part of a discordant pair, so in that case, it counts as both an SR and DR, but is only one independent source of evidence for the variant allele.