<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Hi Nikolas,</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Yes, VEP (as of release/88 and the switch to the ensembl-vep repo) now matches VCF entries based on the alleles present, see [1] and [2].</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">You may disable allele matching by using the “overlap” type instead of “exact”, but this will report entries where any part of the coordinates match between the input and the entry in the VCF (i.e. a SNP will give a match to a long deletion that overlaps it). Perhaps this may not be a concern if excluding data based on coverage is your aim.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Hope that helps</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Will McLaren</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Ensembl Variation</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">[1] : <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html#custom_options">http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html#custom_options</a></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">[2] : <a href="https://github.com/Ensembl/ensembl-vep#differences-to-ensembl-tools-vep">https://github.com/Ensembl/ensembl-vep#differences-to-ensembl-tools-vep</a></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">On 27 June 2017 at 12:24:41, Nikolas Pontikos (<a href="mailto:n.pontikos@ucl.ac.uk">n.pontikos@ucl.ac.uk</a>) wrote:</div> <blockquote type="cite" class="clean_bq"><span><div><div></div><div>
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<div dir="ltr">Dear Developers,
<div><br></div>
<div><span style="line-height:1.5">I want to add custom annotation
to VEP.</span></div>
<div><span style="line-height:1.5">Specifically I want to add the
gnomad coverage downloaded from here:</span></div>
<div><a href="http://gnomad.broadinstitute.org/downloads">http://gnomad.broadinstitute.org/downloads</a><br>
</div>
<div><br></div>
<div>This is important because a colleague pointed out that, at the
moment, it not possible to distinguish between not covered and
covered but zero allele freq in gnomad.</div>
<div><br></div>
<div>My first attempt was to convert to VCF with REF and ALT set to
'X' as they should not be needed by tabix. However this
doesn't work.</div>
<div><br></div>
<div>Does VEP use the REF and ALT in the matching then? I
thought it was simply using positions with tabix.</div>
<div><br></div>
<div>For now, I have converted the per position coverage files to
bed instead and that seems to work ok, although the output is not
as nice.</div>
<div><br></div>
<div>Many Thanks,</div>
<div><br></div>
<div>Nikolas.</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div><br></div>
<div><br></div>
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</div>
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