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Published 20 hours ago • verified publisher icon broadinstitute

Hardcoded HTSJDK JEXL genotype filter bindings not working as expected for VariantFiltration.

Open gokalpcelik opened this issue 7 months ago • 0 comments

Hi

https://gatk.broadinstitute.org/hc/en-us/community/posts/34245458141083-VariantFiltration-isAvailable-and-isNoCall-expressions-for-genotype-filtration-work-unexpectedly

Only isHom, isHet type entries work however isAvailable, isNoCall etc. are not working at all. This could well be a HTSJDK bug but I am not sure. VariantFiltration does not seem to have too much involvement with these hard coded JEXL directly but uses them from HTSJDK.

Issue is reproducible as of GATK 4.6.1.0.

gokalpcelik avatar Mar 03 '25 16:03 gokalpcelik