Support the latest Variant Call Format Specification (VCFv4.3 and BCFv2.2)

[droazen]

Htsjdk does not currently support VCFv4.3 and BCFv2.2. Is there a volunteer in the community who is interested in taking on the task of adding support for the latest spec?

[magicDGS]

I could try it, but I would like to have a list of things that should be done for it.

[fgvieira]

Any news on supporting VCFv4.3 and BCFv2.2 (both for read and write)?

[cmnbroad]

@fgvieira There is both good news and bad news on the status of this. We have a branch and PR with the 4.3 changes that is ready for review, and another branch with the BCF changes. However, both branches are dependent on another large PR with VCFHeader changes, and all of these are going to require a major release and update of htsjdk. We continue to be backlogged on reviewing these large PRs, so the release timeframe is still unclear, but the bulk of the actual work has been done. Thats about all of the clarity I can provide at this time.

[bgulko]

Bump!
It seems that the release when this was reported in 2016 (@droazen) was around 2.2.4. When this thread was updated in 2022 (thanks @cmnbroad !) the release was around 2.24.1. Since then major release 3 was offered mid 2022, and major release 4 was offered in 2023. After a few years and 2 major releases have passed, can BCF2.2 support be incorporated into this library? I understand GATK seems to depend on it and now (2024-Jul) and the widely-used bcftools (1.19) no longer supports BCF versions before 2.2 (release dates found at https://github.com/samtools/htsjdk/releases).

[lindenb]

for those interested, I just wrote a java BCF2.2 parser here: https://github.com/lindenb/bcfparser

For now my unit tests are passing, and there is no difference between the VariantContext generated by htsjdk/VCFFileReader and my parser. Though the raw datatypes in the attributes might change ("1.5" as String vs 1.5 as Float).

I hope it helps