<div dir="ltr">Hi Adam,<div><br></div><div>It's something we're looking at for the next version of the VEP.</div><div><br></div><div>Regards</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><br>
<div class="gmail_quote">On 26 March 2014 17:09, Levine, Adam <span dir="ltr"><<a href="mailto:a.levine@ucl.ac.uk" target="_blank">a.levine@ucl.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-GB" link="blue" vlink="purple">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">I previously enquired about allele specific custom annotation. On a related theme, would it be possible for the VEP to be configured to report the allele frequency (from 1KG and ESP) of the actual alternate
allele as opposed to just the MAF at that position? Obviously, this is important for multiallelic variants and filtering on MAF may result in the exclusion of a rare variant of interest due to the occurrence of a common variant at the same position.<u></u><u></u></span></p>
<div class="">
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Adam<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Adam P. Levine<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
</div><div>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Levine, Adam<br>
<b>Sent:</b> 10 March 2014 15:53</span></p><div><div class="h5"><br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] Allele specific custom annotation<u></u><u></u></div></div><p></p>
</div>
</div><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Dear Will,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you for your prompt reply.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Sure, I will write a script to do it.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Kind regards,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Adam<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Adam P. Levine<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Will McLaren<br>
<b>Sent:</b> 10 March 2014 15:43<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] Allele specific custom annotation<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">Hi Adam,<u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Currently there is no way to do allele-specific annotation with the --custom flag alone.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">If you are not averse to a bit of coding you could write a plugin to do that for you; you could either write the plugin to fetch the scores for you (the VEP is simply piping in tabix output), or have the plugin post-process the scores added
as you have them above (this would require writing the least code).<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html" target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Our dbNSFP plugin does something similar:<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><a href="https://github.com/ensembl-variation/VEP_plugins/blob/master/dbNSFP.pm" target="_blank">https://github.com/ensembl-variation/VEP_plugins/blob/master/dbNSFP.pm</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Regards<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Will McLaren<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Ensembl Variation<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On 10 March 2014 15:30, Levine, Adam <<a href="mailto:a.levine@ucl.ac.uk" target="_blank">a.levine@ucl.ac.uk</a>> wrote:<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">I have a query regarding performing custom annotation using the VEP. I would like to annotate specific allele changes with a score, i.e. a G to T with score X but G to A at the
same position with score Y. It seems, however, that the VEP only annotates on the basis of position and does not consider the allele change. Am I correct? If so, is there a way to set it to use custom annotation tracks in an allele specific manner?<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">The custom annotations are in VCF format, e.g.:<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">##fileformat=VCFv4.0<u></u><u></u></p>
<p class="MsoNormal">#CHROM POS ID REF ALT QUAL FILTER INFO<u></u><u></u></p>
<p class="MsoNormal">21 26960070 GT_scoreX G T . . .<u></u><u></u></p>
<p class="MsoNormal">21 26960070 GA_scoreY G A . . .<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">The input file looks like this:<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">##fileformat=VCFv4.0<u></u><u></u></p>
<p class="MsoNormal">#CHROM POS ID REF ALT QUAL FILTER INFO<u></u><u></u></p>
<p class="MsoNormal">21 26960070 rs116645811 G A . . .<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">My command is:<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">perl
<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> \<u></u><u></u></p>
<p class="MsoNormal">--input_file example_single_variant.vcf \<u></u><u></u></p>
<p class="MsoNormal">--format vcf \<u></u><u></u></p>
<p class="MsoNormal">--custom test_custom.vcf.gz,test_custom,vcf,exact \<u></u><u></u></p>
<p class="MsoNormal">--cache<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">The output looks like this:<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">## ENSEMBL VARIANT EFFECT PREDICTOR v75<u></u><u></u></p>
<p class="MsoNormal">## Output produced at 2014-03-10 14:34:53<u></u><u></u></p>
<p class="MsoNormal">## Connected to homo_sapiens_core_75_37 on
<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a><u></u><u></u></p>
<p class="MsoNormal">## Using cache in /home/Levine/.vep/homo_sapiens/75<u></u><u></u></p>
<p class="MsoNormal">## Using API version 75, DB version 75<u></u><u></u></p>
<p class="MsoNormal">## Extra column keys:<u></u><u></u></p>
<p class="MsoNormal">## DISTANCE : Shortest distance from variant to transcript<u></u><u></u></p>
<p class="MsoNormal">## STRAND : Strand of the feature (1/-1)<u></u><u></u></p>
<p class="MsoNormal">## test_custom : test_custom.vcf.gz (exact)<u></u><u></u></p>
<p class="MsoNormal">#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_ac<u></u><u></u></p>
<p class="MsoNormal">ids Codons Existing_variation Extra<u></u><u></u></p>
<p class="MsoNormal">rs116645811 21:26960070 A ENSG00000260583 ENST00000567517 Transcript upstream_gene_variant - - - -
- - <u></u><u></u></p>
<p class="MsoNormal">STRAND=-1;test_custom=GT_scoreX,GA_scoreY;DISTANCE=4432<u></u><u></u></p>
<p class="MsoNormal">rs116645811 21:26960070 A ENSG00000154719 ENST00000352957 Transcript intron_variant - - - - - -
STRAND=-<u></u><u></u></p>
<p class="MsoNormal">1;test_custom=G_A,G_T<u></u><u></u></p>
<p class="MsoNormal">rs116645811 21:26960070 A ENSG00000154719 ENST00000307301 Transcript missense_variant 1043 1001 334 T/M aCg/aTg -
<u></u><u></u></p>
<p class="MsoNormal">STRAND=-1;test_custom=GT_scoreX,GA_scoreY<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">You can see the variant in the input (G>A) is annotated with both G_A and G_T. I can of course, pull out the relevant annotation (score X for G>T, score Y for G>A) myself manually
after the fact but it would be great if the VEP could do it directly.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Thank you,<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Adam<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Adam P. Levine<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
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<p class="MsoNormal"><u></u> <u></u></p>
</div>
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