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allele depth and depth do not match in my vcf file

I have vcf file where the allele depth and depth do not match. Why is this? Here is the offending line....

chrX 155252833 . G . 81 . DP=12;AD=10;MQSB=0.183296;MQ0F=0.333333;AN=2;DP4=7,3,0,0;MQ=6 GT 0/0

DP is the depth, right? In this example DP is 12. So how come AD is 10?

vcf
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by b10hazard • b10hazard

2 answers

It looks like the AD is only counting high quality reads, while DP counts all the reads. DP4 counts only high quality reads, and it adds up to 10.

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written by swbarnes2 swbarnes2

here is the head of a VCF generated with samtools:

##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">

as you can see for DP4 "Number of high-quality..." and DP Raw read depth

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written by Pierre Lindenbaum Pierre Lindenbaum

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