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SciLifeLab / Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
https://nf-co.re/sarek
MIT License
132 stars 6 forks source link

Annotation with both SnpEff and VEP #792

Closed kokyriakidis closed 4 years ago

kokyriakidis commented 5 years ago

What it the difference between the "merge" option and the "SnpEff,VEP"? Will I see different results?

maxulysse commented 5 years ago

I'm guessing the documentation wasn't clear enough. Sorry about that.

If you specify snpeff,vep, you'll get your VCFs annotated by snpEff, and by VEP, meaning one different annotation for each annotator. If you specify merge, you'll get your VCFs first annotated by snpEff, then the resulting VCFs will be annotated by VEP, meaning final VCFs annotated by both annotators.

https://github.com/SciLifeLab/Sarek/blob/master/docs/ANNOTATION.md