bcftools call -A => segmentation fault

[bcantarel]

I am running into a segmentation fault with bcftools call -A
Similar to what was seen here:
#2118

with
root@4cbb88ec94f0:/data# bcftools --version
bcftools 1.20
Using htslib 1.20
Copyright (C) 2024 Genome Research Ltd.
License Expat: The MIT/Expat license
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Error:
bcftools call -A --threads 8 -g 3 -mO z -o test.sambcf.g.vcf.gz test.mpileup
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
Segmentation fault (core dumped)

Create Correct output:
/usr/local/bin/bcftools call --threads 8 -g 3 -mO z -o test.sambcf.g.vcf.gz test.mpileup
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid

[pd3]

Thank you for the issue. Is there any chance you could provide a small test case to reproduce the error?

[bcantarel]

Unfortunately, I cannot share this sensitive customer data, but I generated the BAM using Giraffe with a pangenome that I created using Cactus-Minigraph.

[pd3]

Any chances you could send the debugging output from valgrind?

[pd3]

Could you perhaps use this script to create a small slice of the bam and the reference https://github.com/pd3/mpileup-tests/blob/main/misc/create-bam-test, as in #2189? The script creates a short artificial chromosome, removes all sample information, and anonymizes the data so that all A,C,G,T bases are randomly shuffled, so that the source region cannot be identified.