Question

ensembl-vep annotation fail

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4.7 years ago

1095937 • 0

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

next-gen vep annotation • 1.2k views

ADD COMMENT • link updated 4.7 years ago by Emily 24k • written 4.7 years ago by 1095937 • 0

score 2 · Answer 1 · 2021-02-01

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4.7 years ago

Emily 24k

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

ADD COMMENT • link 4.7 years ago by Emily 24k

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

ADD REPLY • link 4.7 years ago by brunobsouzaa ▴ 840

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No, only if you output in VCF.

ADD REPLY • link 4.7 years ago by Emily 24k

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

ADD REPLY • link 4.7 years ago by brunobsouzaa ▴ 840