<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">I’m trying to run VEP with the exac plugin over GRCh38:<div><br><div>I’ve isolated a little test-set for a gene (SERPIND1) where I can see Exac variants. </div><div>The actual variant in GRCh38 is:</div><div>22<span class="Apple-tab-span" style="white-space:pre"> </span>20779735 20779735 G/A</div><div><br></div><div>(this is mapped to GRCh37:22:21134023-21134023, which has a lovely synonymous ExAC variant)</div><div><br></div><div>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.</div><div><br></div><div>However when I run via the command line (I include a small.test2.vcf with this single variant):</div><div><br></div><div>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</div><div><br></div><div>- I get no ExAC annotation applied to this single consequence (the last 8 entries of the CSQ field).</div><div><br></div><div>I notice the exac vcf file I put in (indicated via the VEP docs) is the published GRCh37 file from broad.</div><div><br></div><div>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?</div><div><br></div><div>Cheers,</div><div><br></div><div>Vivek</div><div><div><br><div apple-content-edited="true">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">-------------<br>Vivek Iyer<br>Experimental Cancer Genetics<br>Wellcome Trust Sanger Institute<br><a href="mailto:vvi@sanger.ac.uk">vvi@sanger.ac.uk</a><br>+44-1223-495364<br><br><br><br><br><br></div>
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