annotate add INFO/tag form CHROM-POS-REF-ALT
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics, cli
Research direction
Start with the linked “Transfer FILTER values into an INFO tag” annotate howto and the shown bcftools annotate command. Determine whether a single command can construct INFO/raw_pos from CHROM, POS, REF, and ALT without an annotation file; done means the requested command works on the stated VCF input without intermediate files.
Written by the indexing model from the issue text.
Description
i know the
Transfer FILTER values into an INFO tag
bcftools annotate -c INFO/NewTag:=FILTER B.bcf
but i want
bcftools annotate -c INFO/raw_pos:=%CHROM-%POS-%REF-%ALT clinvar_20240902.vcf.gz
# it not work
Is there a simple way to do this? I don't want to use tabix to obtain annotate.gz, because the original VCF is too large, and I always don't want to generate too many intermediate files
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
Contributor guide
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