Question: Annotating varscan2 output
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gravatar for ar.satkhol18
14 months ago by
ar.satkhol180 wrote:

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?

varscan2 annotation • 636 views
ADD COMMENTlink modified 14 months ago by bernatgel2.6k • written 14 months ago by ar.satkhol180
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gravatar for bernatgel
14 months ago by
bernatgel2.6k
Barcelona, Spain
bernatgel2.6k wrote:

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.

ADD COMMENTlink written 14 months ago by bernatgel2.6k

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

ADD REPLYlink written 14 months ago by ar.satkhol180
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