vcf2db without samples

Skip to first unread message

Parkes Kendrick

Feb 1, 2018, 8:43:37 AM2/1/18
to gemini-variation
Hi there,

I annotated a VCF of Clinvar variants using vcfanno and would like to create a database using vcf2db. However, there are no samples in the VCF. I tried adding a fake sample in the header and then making a ped file to go along with this, but am getting an error with this:

File "cyvcf2/cyvcf2.pyx", line 932, in cyvcf2.cyvcf2.Variant.gt_bases.__get__ (cyvcf2/cyvcf2.c:22059)
ValueError: range() step argument must not be zero

I am guessing this is because there are no genotypes? Is there anyway to upload this vcf without samples?


Brent Pedersen

Feb 1, 2018, 9:30:38 AM2/1/18
to Parkes Kendrick, gemini-variation
You could open an issue on the vcf2db repo with a small example VCF
and I'll have a look.
This isn't a target use-case, but we should be able to support it.
Reply all
Reply to author
0 new messages