[ensembl-dev] VEP + ExAC plugin run on GRCh38: website finds ExAC data, command line does not?

[Will McLaren]

Hi Vivek,

You will need a lifted over file.

You can use my copy here:

/nfs/ensembl/wm2/VEP/cache/ExAC.0.3.GRCh38.vcf.gz

Regards

Will

On 4 November 2015 at 14:12, Vivek Iyer <vvi at sanger.ac.uk> wrote:

> I’m trying to run VEP with the exac plugin over GRCh38:
>
> I’ve isolated a little test-set for a gene (SERPIND1) where I can see Exac
> variants.
> The actual variant in GRCh38 is:
> 22 20779735 20779735 G/A
>
> (this is mapped to GRCh37:22:21134023-21134023, which has a lovely
> synonymous ExAC variant)
>
> When I put this variant into the GRCh38 Ensembl web interface, it works a
> treat and recovers the exac data for the single consequence (AF=0.02).
> Hooray, go ensembl.
>
> However when I run via the command line (I include a small.test2.vcf with
> this single variant):
>
> perl /software/vertres/bin-external/variant_effect_predictor_v82.pl
> -offline --vcf --species homo_sapiens --assembly GRCh38 --no_progress
> --everything --cache --pick --dir_cache /data/blastdb/Ensembl/vep  --chr
> chr22 -o small.test2.vep.vcf --force_overwrite -i small.test2.vcf --verbose
> --plugin
> ExAC,/lustre/scratch116/casm/team113/ref/exac/exac.r0.3/ExAC.r0.3.sites.vep.vcf.gz
>
> - I get no ExAC annotation applied to this single consequence (the last 8
> entries of the CSQ field).
>
> I notice the exac vcf file I put in (indicated via the VEP docs) is the
> published GRCh37 file from broad.
>
> Did ensembl produce a 38 remap? The implication is that this should work
> fine for GRCh38 but do I have to lift over the ExAC file myself?
>
> Cheers,
>
> Vivek
>
> -------------
> Vivek Iyer
> Experimental Cancer Genetics
> Wellcome Trust Sanger Institute
> vvi at sanger.ac.uk
> +44-1223-495364
>
>
>
>
>
>
>
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