(DP) Depth value being incorrectly set to 0 for calls

dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects

Apache License 2.0

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(DP) Depth value being incorrectly set to 0 for calls #286

Open carsonhh opened 1 year ago

carsonhh commented 1 year ago

When joint calling gVCF files generated by DeepVariant, GLnexus will assign a genotype of 0/0 and a depth (DP) of 0. However without any supporting reads, the genotype should be './.' or nocall?

Dani-kolbe commented 1 year ago

Same issue here...

carsonhh commented 1 year ago

Any activity here? The issue on the deepvariant side is closed since this is a GLnexus issue after all. The problem is that it creates issues in downstream analysis. Since ./. (no data) is very different from 0/0 (reference genotype). Software that understands pedigrees and inheritance patterns will see 0/0 as evidence against an an expected inheritance pattern which can cause disease gene candidates to be suppressed in a familial analysis.