hiphase/PREFIX.snv.phased.vcf should have the .gz suffix & lacks a .tbi
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Description
Description of the bug
I've just had my first seemingly successful run with pacvar, but a few things standout as odd.
The file named
hiphase/PBSAMP.snv.phased.vcf
is actually gzipped, but the filename does not suggest that.
It does contain the PS "Phase set identifier" and that value is populated on many rows. However the files
deepvariant/PBSAMP.snv.vcf.gz and
deepvariant/PBSAMP.snv.g.vcf.gz
have PS only in their header, not on any rows.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by tracing how hiphase/PBSAMP.snv.phased.vcf is produced and how the deepvariant/PBSAMP.snv.vcf.gz and deepvariant/PBSAMP.snv.g.vcf.gz outputs are named and indexed. Check the generated files to confirm compression, PS-field behavior, and whether a .tbi index is created. Done means the phased VCF has the .gz suffix, a matching .tbi exists, and the intended PS output is consistent.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 55/100