Filtering of VCF, INFO DP or FORMAT DP

Question

[waqasnayab]

Hi,

I have a confusion regarding the filtering of VCF file. Consider the line below:

chr1    14464   rs546169444 A   T   112.33  .   AC=1;AF=0.125;AN=8;BaseQRankSum=0.548;ClippingRankSum=0.000;DB;DP=123;ExcessHet=3.0103;FS=1.574;MLEAC=1;MLEAF=0.125;MQ=28.09;MQRankSum=0.745;QD=2.88;ReadPosRankSum=2.036;SOR=0.344 GT:AD:DP:GQ:PL  0/1:31,8:39:99:144,0,845    0/0:27,0:27:81:0,81,799 0/0:30,0:30:90:0,90,847 0/0:27,0:27:81:0,81,799

There are two DP, one in INFO field DP=123 while the other is in FORMAT field. As it has four samples so each sample has its own DP in FORMAT field: 39, 81, 30, and 27.

My confusions are:

1. The additive of DP of the FORMAT field is not 123, why is the difference???,

2. If we filter vcf file on the basis of DP, which DP would the filtering tool used, INFO's DP or FORMAT's DP?

Thanks in advance,

Waqas.

Answer 1

[Pierre Lindenbaum]

https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_annotator_Coverage.php

"At the sample level (FORMAT), the DP value is the count of reads that passed the caller's internal quality control metrics (such as MAPQ > 17, for example)."

.

"At the site level (INFO), the DP value is the unfiltered depth over all samples."

.

If we filter vcf file on the basis of DP, which DP would the filtering tool used, INFO's DP or FORMAT's DP?

depends of our needs...