bcftools -C alleles segment fault

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start by reproducing the supplied bcftools mpileup and bcftools call -C alleles pipeline with dbsnp138.targets.tsv.gz, human_g1k_v37_decoy.fasta, and sample.bam. Inspect the failure in the -C alleles calling path and capture the bcftools version and a debugger backtrace; done means the command no longer segfaults on the reported inputs.

Written by the indexing model from the issue text.

Description

requires-test-case

hi

I want to use bcftools to call dbsnp variants, here is my command

creage targets, dbsnp chrom is GRCh37-like

bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n'  dbsnp138.vcf.gz \
| bgzip -c > dbsnp138.targets.tsv.gz && tabix -s1 -b2 -e2 dbsnp138.targets.tsv.gz

call variants

bcftools mpileup -R dbsnp138.targets.tsv.gz  \
           -f  human_g1k_v37_decoy.fasta \
            sample.bam \
           | bcftools call -C alleles -T dbsnp138.targets.tsv.gz \
            -m -o sample.bcftools.vcf.gz

the command will run a while, but then throw error 'segment fault'

Dominant language
C
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