Question: PISCES DP is greater than AD
gravatar for rosefroehlich
5 months ago by
rosefroehlich0 wrote:


I am using Pisces for variant calling in my TST170 data and have a question regarding the AD and DP values in the vcf. Why is the DP value greater than the sum of the two given AD values for the Alt and Reference Allele? Reading the following on Github made me think that the DP-AD(Alt)=AD(Ref): "Coverage at a particular location is calculated as the sum of all called reads which pass filters (have sufficient mapping quality and base call quality). Coverage is given as DP in the vcf file. Deleted bases have counted towards coverage since version 3.5.5 . SNV count uses the same filters as the coverage count filters. Indel/MNV count is the sum of all reads passing filters where we were able to determine an indel/MNV. The estimate reference count is the coverage minus the variant count. (So, for an indel or MNV, the "reference count" is really the total number of passing reads that did not have the given variant). Variant frequency is calculated by dividing the variant count by the coverage at the given location*.“

I would be very thankful for you help.

Best regards, Rose

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