Bcftools merge fails parsing
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- aws, c
- Domain
- bioinformatics, cloud
Research direction
Start at the bcftools merge command described in the report and reproduce it with indexed VCFs from AWS S3, a regions text file, an S3 path list, and the -m snps option. Inspect the [E::get_intv] TBX_VCF warning while comparing the first input with later inputs. Done means subsequent VCF fields are parsed and merged rather than empty.
Written by the indexing model from the issue text.
Description
I’ve been getting issues trying to merge multiple VCFs from AWS S3 buckets that have been indexed using tabix. When I run the command, I give it regions from a text file, S3 paths in a text file, give it the “-m snps” flag and an output file name. The first VCF in the file has no issues, but the subsequent VCFs’ fields are empty. When I pull the VCFs individually, the VCFs all pull fine, and when I change the order of the S3 path list, the first file in the new list works but the rest don’t. I also get some errors/warnings printed in the command line if it means anything “[E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?” These are standard VCFs generates by GATK. Any insight?
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
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