<div dir="ltr">Hi Andrew,<div><br>The VEP deals with sequence variants and structural variants slightly differently.</div><div><br></div><div>The first line is being interpreted as a structural variant since the INFO column contains the <span style="font-family:Calibri,sans-serif;font-size:15px">SVLEN and </span><span style="font-family:Calibri,sans-serif;font-size:15px">SVTYPE fields; the second is being interpreted as a sequence variant since these fields are absent and you have the ref and alt sequence defined.</span></div>
<div><span style="font-family:Calibri,sans-serif;font-size:15px"><br></span></div><div><span style="font-family:Calibri,sans-serif;font-size:15px">--pick has not been extended to work with SVs yet, hence why you are seeing multiple annotations for 1).</span></div>
<div><span style="font-family:Calibri,sans-serif;font-size:15px"><br></span></div><div><span style="font-family:Calibri,sans-serif;font-size:15px">VEP's annotation is richest for sequence variants, since when a variant is parsed as a structural variant the sequence is not considered, just the coordinates. So in this case I'd recommend you remove the SVLEN and SVTYPE fields when you have the sequence in the REF and ALT fields.</span></div>
<div><span style="font-family:Calibri,sans-serif;font-size:15px"><br></span></div><div><span style="font-family:Calibri,sans-serif;font-size:15px">Hope that helps</span></div><div><span style="font-family:Calibri,sans-serif;font-size:15px"><br>
</span></div><div><span style="font-family:Calibri,sans-serif;font-size:15px">Will McLaren</span></div><div><span style="font-family:Calibri,sans-serif;font-size:15px">Ensembl Variation</span></div><div><br></div><div><br>
</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 16 April 2014 23:06, Andrew Carson <span dir="ltr"><<a href="mailto:acarson@invivoscribe.com" target="_blank">acarson@invivoscribe.com</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-US" link="blue" vlink="purple"><div><p class="MsoNormal">Hi,<u></u><u></u></p><p class="MsoNormal">I noticed some strange behavior when annotating variants from different variant calling strategies. Basically, I call the same variant by 2 different strategies, but I get different annotations from VEP. The only difference between the two input variants is in the INFO/FORMAT/Genotype fields of the vcf file. But, for one of the outputs, the --pick option is not working. And there are some clear differences in the output.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Here is an example:<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Input 1)<u></u><u></u></p><p class="MsoNormal">13 28602226 . AAG A . PASS END=28602228;HOMLEN=20;HOMSEQ=AGAGAGAGAGAGAGAGAGAG;SVLEN=-2;SVTYPE=DEL GT:AD 0/1:49<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Input 2)<u></u><u></u></p><p class="MsoNormal">13 28602226 . AAG A . PASS ADP=72;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:255:72:72:2:66:91.67%:4.0594E-37:33:32:1:1:40:26<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">As you can see, the only differences occur after column 8, but I don’t think these should affect the annotation of the deletion.<u></u><u></u></p><p class="MsoNormal">
<u></u> <u></u></p><p class="MsoNormal">When I run these two inputs through VEP using the following command:<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">perl /path/to/vep --fork 4 --no_stats --everything --cache -i input.vcf -o outpu.VEP.vcf --format vcf --force_overwrite --check_existing --check_alleles --vcf --no_progress --pubmed --gmaf --maf_1kg --pick <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">I get the following:<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Output 1)<u></u><u></u></p><p class="MsoNormal">13 28602226 . AAG A . PASS END=28602228;HOMLEN=20;HOMSEQ=AGAGAGAGAGAGAGAGAGAG;SVLEN=-2;SVTYPE=DEL;CSQ=deletion|ENSG00000122025|ENST00000380987|Transcript|intron_variant&NMD_transcript_variant&feature_truncation||||||||||16/24||||||-1|||FLT3|HGNC||||nonsense_mediated_decay|ENSP00000370374|||||||||,deletion|ENSG00000122025|ENST00000241453|Transcript|intron_variant&feature_truncation||||||||||16/23||||||-1||YES|FLT3|HGNC||||protein_coding|ENSP00000241453||CCDS31953.1|||||||,deletion|ENSG00000122025|ENST00000537084|Transcript|intron_variant&feature_truncation||||||||||16/22||||||-1|||FLT3|HGNC||||protein_coding|ENSP00000438139|||||||||,deletion|ENSG00000122025|ENST00000380982|Transcript|intron_variant&feature_truncation||||||||||16/23||||||-1|||FLT3|HGNC||||protein_coding|ENSP00000370369||||||||| GT:AD 0/1:49<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Output 2)<u></u><u></u></p><p class="MsoNormal">13 28602226 . AAG A . PASS ADP=72;WT=0;HET=1;HOM=0;NC=0;CSQ=-|ENSG00000122025|ENST00000241453|Transcript|intron_variant&feature_truncation||||||rs60462219||||16/23||||||-1||YES|FLT3|HGNC||||protein_coding|ENSP00000241453||CCDS31953.1|ENST00000241453.7:c.2053+87_2053+88delCT|||||| GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:255:72:72:2:66:91.67%:4.0594E-37:33:32:1:1:40:26<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">As you can see, the first output isn’t using --pick as it outputs multiple annotations. In addition, the annotations are slightly different from the “pick”d variant in output 2. The consequence changes from “deletion” to “-“. And in output 2, I get the CDS: “ENST00000241453.7:c.2053+87_2053+88delCT” which is not provided in the annotation of output 1.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Is there are reason for this discrepancy? Is there something I can do to avoid getting these differences? Is my input or commands incorrect in this instance?<br>
<br>Any help would be greatly appreciated.<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"><span style="font-family:"Myriad Pro","sans-serif"">Andrew R. Carson, Ph.D.</span> <u></u><u></u></p>
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<br></blockquote></div><br></div>