Annotating varscan2 output

Question

[ar.satkhol18]

Hi, I have a vcf file of somatic variants from Varscan2. I tried annotating it with Variant Effect Predictor and snpEff. The online version of VEP gives an empty output. snpEff takes too long to run, more than 6 hrs. Can anybody suggest an alternative tool for annotating Varscan vcf ? Is there any way I can convert the vcf to a format acceptable by VEP or snpEFF?

Answer 1

[bernatgel]

We have used annovar to annotate VarScan results in VCF. It works quite well and is widely used.

You'll need to decide what you want to annotate and download the annovar databases from the annovar website before running it.

[ar.satkhol18]

Okay, I'll try annotating with annovar. Thank you