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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?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">The custom annotations are in VCF format, e.g.:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">##fileformat=VCFv4.0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">#CHROM POS ID REF ALT QUAL FILTER INFO<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">21 26960070 GT_scoreX G T . . .<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">21 26960070 GA_scoreY G A . . .<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">The input file looks like this:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">##fileformat=VCFv4.0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">#CHROM POS ID REF ALT QUAL FILTER INFO<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">21 26960070 rs116645811 G A . . .<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">My command is:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">perl variant_effect_predictor.pl \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">--input_file example_single_variant.vcf \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">--format vcf \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">--custom test_custom.vcf.gz,test_custom,vcf,exact \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">--cache<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">The output looks like this:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## ENSEMBL VARIANT EFFECT PREDICTOR v75<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## Output produced at 2014-03-10 14:34:53<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## Connected to homo_sapiens_core_75_37 on ensembldb.ensembl.org<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## Using cache in /home/Levine/.vep/homo_sapiens/75<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## Using API version 75, DB version 75<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## Extra column keys:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## DISTANCE : Shortest distance from variant to transcript<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## STRAND : Strand of the feature (1/-1)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">## test_custom : test_custom.vcf.gz (exact)<o:p></o:p></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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">ids Codons Existing_variation Extra<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">rs116645811 21:26960070 A ENSG00000260583 ENST00000567517 Transcript upstream_gene_variant - - - - -
- <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">STRAND=-1;test_custom=GT_scoreX,GA_scoreY;DISTANCE=4432<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">rs116645811 21:26960070 A ENSG00000154719 ENST00000352957 Transcript intron_variant - - - - - -
STRAND=-<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">1;test_custom=G_A,G_T<o:p></o:p></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 -
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">STRAND=-1;test_custom=GT_scoreX,GA_scoreY<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">Thank you,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">Adam<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-GB">Adam P. Levine</span><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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