Vcf_combiner - HailException: RVD error! Keys found out of order:

I am running locally on 500 vcfs (not gvcf) and I’ve got this error:

RVD error! Keys found out of order:
Current key: {locus: {contig: chrM, position,41},alleles: [2;C,G] }
Previous key: {locus: {contig: chrM, position,41},alleles: [2;C,T] }

How can I avoid this. How can I effectively combine vcf to one matrix table?

Thank you Radim

The VCF combiner really isn’t designed to work on VCFs, only GVCFs. In particular, the problem here – I believe – is that you have one or more input VCFs with duplicate loci from split multiallelics. This breaks the data model of the VCF combiner.

1 Like