AD 0,0 BUT DP >0

kullrichkullrich GermanyMember
edited June 2016 in Ask the GATK team

Hi I would have a question regarding the GATK output applying all steps and doing a multiple sample calling.

There are some entries which apparently have a AD: 0,0 for the REF and ALT allele but have a DP value greater than 0.

How can this be?

Even the GT field is sometimes in this cases set to 0/0 or 1/1 is this arbitrary?

Thank you in anticipation for answering the question

solved

just found this entry

http://gatkforums.broadinstitute.org/gatk/discussion/6005/allele-depth-ad-is-lower-than-expected

Post edited by kullrich on
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