INDELs VEP anntotation Consequence is missense_variant

Open pl618 opened this issue 6 years ago • 2 comments

https://github.com/bm2-lab/pTuneos/blob/e6cfd0e1b57bf04fe60baee40efe4f3b0c8d56f3/src/core/VariantCallingFormat/VCFprocessor.py#L72

For INDELs, it seems that no Consequence is missense_variant ?

Apr 22 '20 02:04 pl618

https://github.com/bm2-lab/pTuneos/blob/e6cfd0e1b57bf04fe60baee40efe4f3b0c8d56f3/src/core/VariantCallingFormat/VCFprocessor.py#L72

For INDELs, it seems that no Consequence is missense_variant ?

I think so. The Consequence is always frameshift or some else.

Jul 29 '20 02:07 renyongzhe

Hi, all You both are right!

Actually, Consequence for INDEL should be "coding_sequence_variant" and in the VEP annotation results, it might be "frameshift_variant" or "inframe_deletion" or something orther. We have modified it and test it in several datasets. Thank you for your feedback.

Best， Chi

Aug 04 '20 08:08 ChiZhou-SITI