<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 12 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"Myriad Pro";
panose-1:2 11 5 3 3 4 3 2 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Balloon Text Char";
margin:0in;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-priority:99;
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Hi,<o:p></o:p></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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Here is an example:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Input 1)<o:p></o:p></p><p class=MsoNormal>13 28602226 . AAG A . PASS END=28602228;HOMLEN=20;HOMSEQ=AGAGAGAGAGAGAGAGAGAG;SVLEN=-2;SVTYPE=DEL GT:AD 0/1:49<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Input 2)<o:p></o:p></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<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>When I run these two inputs through VEP using the following command:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></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 <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I get the following:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Output 1)<o:p></o:p></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<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Output 2)<o:p></o:p></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<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></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.<o:p></o:p></p><p class=MsoNormal>Thank you!<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='font-family:"Myriad Pro","sans-serif"'>Andrew R. Carson, Ph.D.</span> <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>