Duplicated Loci error on VDS Combiner

Hail Query & hailctl
1

Hello Hail team,

I was trying to create a VDS from a set of GVCF files and got the following error:

Hail version: 0.2.78-b17627756568
Error summary: HailException: RVD error! Keys found out of order:
  Current key:  { locus: { contig: chrM, position: 152 }, alleles: [2; T, A] }
  Previous key: { locus: { contig: chrM, position: 152 }, alleles: [2; T, C] }
This error can occur after a split_multi if the dataset
contains both multiallelic variants and duplicated loci.

Then I found that this error is a known issue (my GVCFs were also generated by DRAGEN):

Is there any update on this issue?

Thank you,
Rodrigo

2

@chrisvittal

3

This is WONTFIX. Hail’s VDS combiner does not support duplicate loci in GVCFs.

4

I understand, so there is no option for interval filtering while creating new VDS, as proposed before?

Thank you for the support!