bcftools call with -T only works with .vcf.gz; not bcf
Nobody has claimed this yet.
Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 38/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Reproduce the reported command using samtools mpileup piped to bcftools call with -T pointing to a .bcf file, comparing it with the stated .vcf.gz behavior. Start at bcftools call's -T target-file handling; done means the command no longer segfaults when the target file is BCF.
Written by the indexing model from the issue text.
Description
Here is what I am running:
samtools mpileup -t DP,DV,DP4,SP -g -f ../reference/ce10/ce10.fa -r chrI JU2464.bam | bcftools call -T ../individual_bcf/complete_variant_set.bcf --format-fields GQ,GP -c -v > ../group_bcf/raw.JU2464.chrI.group.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
Segmentation fault
Results in a segmentation fault.
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
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