Question

What does CSQ means in a VCF file annotated by VEP ?

5

Entering edit mode

6.7 years ago

乙 ▴ 240

Hello,

I have annotated a VCF file using VEP by Ensembl. I have been trying to look over the internet the meaning of CSQ that can be found in the headers:

enter image description here

Do you know the meaning of CSQ ?

Thanks

VCF CSQ • 6.5k views

ADD COMMENT • link updated 6.7 years ago by WouterDeCoster 48k • written 6.7 years ago by 乙 ▴ 240

score 6 · Accepted Answer · 2019-03-12

6

Entering edit mode

6.7 years ago

WouterDeCoster 48k

The meaning of CSQ is described in that line. It starts with "Consequence an..." and you clipped off the rest in your screenshot.

Googling CSQ VEP brings me immediately to https://www.ensembl.org/info/docs/tools/vep/vep_formats.html

ADD COMMENT • link 6.7 years ago by WouterDeCoster 48k

2

Entering edit mode

Thanks for your reply. The rest of the screenshot is the follow:

##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP.

I don't think this correspond to the abbreviation of CSQ. I also stumbled on the page you provided however there's really no definition for that acronym.

I just though about it. Maybe this stands simply for ConSeQuences.

ADD REPLY • link 6.7 years ago by 乙 ▴ 240

2

Entering edit mode

I just though about it. Maybe this stands simply for ConSeQuences.

I'd think you're right.

ADD REPLY • link 6.7 years ago by WouterDeCoster 48k