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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><font size="2" color="black" face="Tahoma"><span style="font-size:10pt;" dir="ltr">Hello,<br>
<br>
I have a VCF file that I have annotated with Annovar, and I have been experimenting with adding VEP's annotations to this VCF. I am having some difficulty since Annovar will occasionally introduce spaces into the INFO field, and VEP is having a hard time handling
these.<br>
<br>
I am aware that VEP only supports VCF format 4.0 (source: <a href="http://useast.ensembl.org/info/docs/tools/vep/vep_formats.html)," target="_blank">
http://useast.ensembl.org/info/docs/tools/vep/vep_formats.html),</a> which does not allow spaces in the INFO field (alphanumeric string, see
<a href="http://www.internationalgenome.org/wiki/Analysis/vcf4.0/" target="_blank">
http://www.internationalgenome.org/wiki/Analysis/vcf4.0/</a>). Thus, Annovar's annotations and VEP are technically incompatible, but I would like to explore using both.<br>
<br>
I have attached a single-line VCF with very minimal information (space.vcf). In it, one of the annotations in the INFO field contains a space ("VT=nonsynonymous SNV"). If I attempt to decompose the VCF and annotate it with VEP (see attached script "vep.sh"),
VEP will add its annotations to a "CSQ" field, but will interpret the space as the end of all INFO annotations, and will convert the space into a tab. Of course, this will introduce a new column, which breaks the rest of my tooling. See below:<br>
<br>
Original variant:<br>
<br>
1 877831 rs6672356 T C 1413.77 PASS VT=<b>nonsynonymous SNV</b> GT:AD:DP:GQ:PL 1/1:0,48:48:99:1442,144,0<br>
<br>
Annotated variant:<br>
<br>
1 877831 rs6672356 T C 1413.77 PASS VT=<b>nonsynonymous;CSQ=<vep info here...></b><i><new TAB here></i><b>SNV</b> GT:AD:DP:GQ:PL 1/1:0,48:48:99:1442,144,0<br>
<br>
<br>
VEP introduces a tab before "SNV", which creates a new column. It appears as though VEP is scanning the columns by whitespace (which includes spaces) instead of by TAB only. Are there any solutions you can recommend? At the moment, I am replacing spaces
with underscores, but this appears to be an inelegant solution. Any suggestions are appreciated.<br>
<br>
Thanks,<br>
Noah Reinhardt<br>
Research Trainee in Computational Medicine<br>
The Hospital for Sick Children<br>
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