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Running bcftools mpileup --indels-2.0 fails in combination with --no-reference

Open fd-bnt opened this issue 2 years ago • 1 comments

Either option without the other specified finished successfully, but in combination results in:

$ bcftools mpileup -B --no-reference -d 200000 -L 200000 --indels-2.0 -o noref.mpileup.vcf anon_slice.sam
[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 200000
bcftools: bam2bcf_iaux.c:703: bcf_iaux_gap_prep: Assertion `!(ref == 0 || bca == 0)' failed.
Aborted (core dumped)

fd-bnt avatar Jun 12 '23 09:06 fd-bnt

Uh, the functionality of --indels-2.0 relies heavily on the reference genome, at the moment it cannot work without it.

pd3 avatar Jun 16 '23 08:06 pd3