I have a use-case where I'd like to merge BCF files with the REF/ALT fields unset, which returns a segmentation fault. The following contains two simple BCF files (and their .csi indexes) to illustrate: test.tar.gz

Running bcftools view on either file looks fine, but

> bcftools merge first.bcf second.bcf
[1]    23882 segmentation fault (core dumped)  bcftools merge first.bcf second.bcf

Setting the REF/ALT fields in each BCF fixes the problem. Also, converting to VCF first seems to work, i.e. the following runs fine:

> bcftools view first.bcf | bgzip > first.vcf.gz && tabix first.vcf.gz                                                                                                           
> bcftools view second.bcf | bgzip > second.vcf.gz && tabix second.vcf.gz                                                                                                         
> bcftools merge first.vcf.gz second.vcf.gz

However, for the application I have in mind, converting via VCF is not an option, unfortunately.

At first, I was unsure whether the BCF specs permit unset REF/ALT, but since writing the BCF (using htslib bindings) and other bcftools commands appear to work, I'm thinking this is not the problem?