In my VCF file from GATK, I have the following definitions for AD and DP.

AD - Allelic depths for the ref and alt alleles in the order listed
DP - Approximate read depth (reads with MQ=255 or with bad mates are filtered

I don't understand the definitions, can anybody explain in a less technical way?

From what I can read, AD gives the number of reads spanning the reference and variant allele. But what does DP mean? This doesn't look like the total number of reads spanning a variant, so what is this? How does this different to AD?


DP is the total number of read bases spanning a particular position. If you add up the different AD, you should get a number close to DP, the difference being merely in how the reads are filtered in either set of numbers.


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