ensembl-vep annotation fail

Question

[1095937]

I annotated my WES data using the web version of ensembl-vep. Most of the variants, some of which have been reported as Known, i.e. with rs numbers have no annotation data. why is this? for example, I have variant; rs13303056: 1:930939-930939, but no other information for the variant

Answer 1

[Emily]

The web version of the VEP is not suitable for WES data. For data at that scale you need to use the offline version.

[brunobsouzaa]

Hi Emily. Is there a way to keep VCF fields QUAL and FILTER when using tab output format from command-line Ensembl VEP?

[Emily]

No, only if you output in VCF.

[brunobsouzaa]

Ok.. Thanks. I've found a simple awk solution for this task.