This is a test version of Biostars. For the public version, visit https://www.biostars.org.
simple question about insertion standards in vcf 4.2

I am having a bit of a hard time understanding why the insertion example in #3 in 5.1.1 (link below) has a TC for REF. Why would it not just be C or the base before the event and then ALT just be CA? What am I missing here? Thank you!

https://imgur.com/a/R3ck2f5

vcf specificaiton
• 1,160 views • link
updated by chrchang523 chrchang523 • written by curious curious

This looks like a multi-allelic entry (like chrchang says) that was split but not subjected to left alignment + parsimony.

• 0 views • link
written by Ram Ram

1 answer

I don't think you're missing anything; the REF=TC choice only makes sense if the deletion and insertion are being reported in the same variant (REF=TC, ALT=T,TCA), and the specification makes no mention of that.

Feel free to create an issue at https://github.com/samtools/hts-specs/issues .

• 0 views • link
written by chrchang523 chrchang523

Thanks! I did wonder if it was a mistake

• 0 views • link
written by curious curious

Log in to answer this question.

More posts like this