Clinvar annotation error


#1

Hi,

We’re using Hail 0.2 and we’re trying to annotate a vcf with Clinvar’s latest version (clinvar_20190211.vcf.gz). When we try to import ClinVar’s vcf we get the following error:

Caused by: is.hail.utils.HailException: hg37_clinvar_20180930.vcf.bgz: Invalid locus NW_003315947.1:181683' found. Contig NW_003315947.1’ is not in the reference genome `GRCh37’.
offending line: NW_003315947.1 181683 156304 C G . . ALLELEID=166084;CLNDISD…

We didn’t process the file, we just ran ‘import_vcf’ with the raw data path. Is this a known issue?
Thank you so much,

Cristina.


#2

Hi Cristina, NW_003315947.1 is indeed not a known contig. You can skip invalid loci by setting skip_invalid_loci=True.


#3

Thanks so much!!