manta icon indicating copy to clipboard operation
manta copied to clipboard

Published 20 hours ago • verified publisher icon Illumina

VCFv4.2

Open curtisjamison opened this issue 6 years ago • 3 comments

Any chance you'll be upgrading the output to VCFv4.2? vcftools vcfconvert doesn't like the ALT designations and won't update the file.

Thanks, Curt

curtisjamison avatar Feb 22 '19 02:02 curtisjamison

Can you please give an example about the complain of ALT?

x-chen avatar Mar 11 '19 18:03 x-chen

I've already spoken a bit with Chris S about this. The issue comes when vcfconvert encounters a deletion such as REF:CAG -> ALT:C. The anchor base at the beginning confuses vcfconvert, because it is expecting REF:AG -> ALT:"-", and it throws an error.

The root cause lies with vcfconvert. However, I was hoping you were going to have an upgrade at some point to VCFv4.2 so I wouldn't have to mess around with vcfconvert.

curtisjamison avatar Mar 11 '19 20:03 curtisjamison

Probably no plans to go to VCF4.2 until we need to use a 4.2-only feature. The prefix base is still being used in VCF4.2 for a small indel style (ie. non-symbolic ALT) variant.

I think the current output should be 4.2 compatible, so can you just change the version number in the VCF headers?

ctsa avatar Jul 09 '19 21:07 ctsa