Question

allele depth and depth do not match in my vcf file

0

Entering edit mode

6.7 years ago

b10hazard ▴ 30

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 • 2.8k views

ADD COMMENT • link updated 6.7 years ago by Pierre Lindenbaum 164k • written 6.7 years ago by b10hazard ▴ 30

score 4 · Accepted Answer · 2018-03-16

4

Entering edit mode

6.7 years ago

swbarnes2 14k

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.

ADD COMMENT • link 6.7 years ago by swbarnes2 14k

score 4 · Accepted Answer · 2018-03-16

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