I noticed that get_vcf_metadata doesn’t appear to be pulling the descriptions of FILTER lines. For example, I ran: metadata = hl.get_vcf_metadata( 'gs://gnomad-public/release/2.1.1/liftover_grch38/vcf/exomes/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz') The VCF has the following descrip…

huh, weird. We can take a look.

aha… hail-is/hail/blob/a1743a3e75d40506349bc0595c43a3769cfb8371/hail/src/main/scala/is/hail/io/vcf/LoadVCF.scala#L1201-L1207 // FIXME apply descriptions when HTSJDK is fixed to expose filter descriptions val filterAttrs: VCFAttributes = header .getFilterLines .toList // (ID, descrip…

I am having a similar issue with hail 0.2.70 for the format and and info field. Doesn’t look like it got resolved. hail-0.2.70-4fcd186e31da After uploading vcfs, merging to mt, qcing and exporting back to vcf, the header was missing the filled out Description field for the FORMAT and INFO header …

Hail does not track these descriptions internally. If you want to include header metadata, you can supply that with the metadata argument of export_vcf. The expected value here is a dictionary – you can use the desciptions/numbers from some existing VCF by using hl.get_vcf_metadata and passing the …

Get_vcf_metadata omitting FILTER line descriptions

Hail Query & hailctl

tpoterba October 10, 2019, 1:40pm 4

https://github.com/hail-is/hail/pull/7244 will fix

Topic		Replies	Views
Export VCF header Hail Query & hailctl	1	451	November 15, 2019
Exporting Hail MT to VCF - FORMAT columns missing Hail Query & hailctl	3	142	March 31, 2025
Best strategy for annotating and filtering VCF files using HAIL-VEP on UKB RAP? Hail Query & hailctl	3	1809	June 17, 2022
Export_vcf(): Invalid type for format field 'gvcf_info' Hail Query & hailctl	12	1012	July 23, 2020
Export_vcf with VEP Hail Query & hailctl	8	1188	May 12, 2021

Get_vcf_metadata omitting FILTER line descriptions

Related topics