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ensembl-vep annotation fail

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
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updated by Emily Emily • written by 1095937 • 1095937

1 answer

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

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written by Emily Emily

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

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written by brunobsouzaa brunobsouzaa

No, only if you output in VCF.

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written by Emily Emily

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

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written by brunobsouzaa brunobsouzaa

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