Ensembl variant effect predictor bigWigToWig

Question

[jeno0726]

Hi!

I want to annotate my vcf file with GERP scores. I found that ensembl have variant effect predictor that should be able to do this pretty easy with the following row (also found at http://www.ensembl.org/info/docs/tools/vep/script/vep_example.html):

perl variant_effect_predictor.pl -cache -i example.vcf -custom All_hg19_RS.bw,GERP,bigwig

When I try to run it it gives the error message:

ERROR: bigWigToWig does not seem to be in your path - this is required to use bigwig format custom annotations

Anybody have a suggestion on how I can get the bigWigToWig to be in my path?

Thanks,
Jessika

Answer 1

[EnsemblWill]

bigWigToWig is part of the UCSC kent source tree

See this page for installation instructions: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/README.building.source