<div dir="ltr">Hi Adam,<div><br></div><div>Currently there is no way to do allele-specific annotation with the --custom flag alone.</div><div><br></div><div>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).</div>
<div><br></div><div><a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html">http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html</a><br></div><div><br></div><div>Our dbNSFP plugin does something similar:</div>
<div><br></div><div><a href="https://github.com/ensembl-variation/VEP_plugins/blob/master/dbNSFP.pm">https://github.com/ensembl-variation/VEP_plugins/blob/master/dbNSFP.pm</a><br></div><div><br></div><div>Regards</div><div>
<br></div><div>Will McLaren</div><div>Ensembl Variation</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 10 March 2014 15:30, 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">
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<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">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></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">The custom annotations are in VCF format, e.g.:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">##fileformat=VCFv4.0<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">#CHROM POS ID REF ALT QUAL FILTER INFO<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">21 26960070 GT_scoreX G T . . .<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">21 26960070 GA_scoreY G A . . .<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">The input file looks like this:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">##fileformat=VCFv4.0<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">#CHROM POS ID REF ALT QUAL FILTER INFO<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">21 26960070 rs116645811 G A . . .<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">My command is:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> \<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">--input_file example_single_variant.vcf \<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">--format vcf \<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">--custom test_custom.vcf.gz,test_custom,vcf,exact \<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">--cache<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">The output looks like this:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## ENSEMBL VARIANT EFFECT PREDICTOR v75<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## Output produced at 2014-03-10 14:34:53<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## Connected to homo_sapiens_core_75_37 on <a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## Using cache in /home/Levine/.vep/homo_sapiens/75<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## Using API version 75, DB version 75<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## Extra column keys:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## DISTANCE : Shortest distance from variant to transcript<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## STRAND : Strand of the feature (1/-1)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## test_custom : test_custom.vcf.gz (exact)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_ac<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">ids Codons Existing_variation Extra<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">rs116645811 21:26960070 A ENSG00000260583 ENST00000567517 Transcript upstream_gene_variant - - - - -
- <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">STRAND=-1;test_custom=GT_scoreX,GA_scoreY;DISTANCE=4432<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">rs116645811 21:26960070 A ENSG00000154719 ENST00000352957 Transcript intron_variant - - - - - -
STRAND=-<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">1;test_custom=G_A,G_T<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">rs116645811 21:26960070 A ENSG00000154719 ENST00000307301 Transcript missense_variant 1043 1001 334 T/M aCg/aTg -
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">STRAND=-1;test_custom=GT_scoreX,GA_scoreY<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">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></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">Thank you,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">Adam<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">Adam P. Levine</span><span style="font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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