<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Hi Matthew,</div> <br> <div id="bloop_sign_1502093699561300992" class="bloop_sign"></div> <br><p class="airmail_on">On 4 August 2017 at 22:33:12, Maher, Matthew (<a href="mailto:matthew_maher@meei.harvard.edu">matthew_maher@meei.harvard.edu</a>) wrote:</p> <div><blockquote type="cite" class="clean_bq" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"><span><div><div></div><div>1. Is this the correct forum for asking a question about VEP<span class="Apple-converted-space"> </span><br>functionality? if not, what is?<span class="Apple-converted-space"> </span></div></div></span></blockquote></div><p>Yes, it is!</p><div><div><blockquote type="cite" class="clean_bq" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"><span><div><div><br><br>2. In VEP, with --vcf output in use, invoking --custom annotations<span class="Apple-converted-space"> </span><br>seems to result in the new/custom values being added as new positional<span class="Apple-converted-space"> </span><br>values within the CSQ/ANN structure - and that structure can have any #<span class="Apple-converted-space"> </span><br>of value sets (possibly zero? I'm not sure). The result of this<span class="Apple-converted-space"> </span><br>placement seems to be the new/custom annotations being unnecessarily<span class="Apple-converted-space"> </span><br>repeated (since they apply to the position, not the specific transcript<span class="Apple-converted-space"> </span><br>annotations) and potentially missed completely (in the case of no CSQ<span class="Apple-converted-space"> </span><br>entries). Is there an option (I can't find it) to cause the new/custom<span class="Apple-converted-space"> </span><br>annotation to appear as a new standalone KEY=[VALUE,VALUE,...] entry in<span class="Apple-converted-space"> </span><br>the INFO field (outside of the CSQ entry), with a VCF header entry<span class="Apple-converted-space"> </span><br>indicating "Number=A" (one value per alternate allele)?<span class="Apple-converted-space"> </span></div></div></span></blockquote></div><p>—custom annotations are added to the CSQ/ANN structure. There’s currently no way to force VEP to write them as separate INFO fields. How many fields added depends on the file format of your custom annotations and any options you select. The fields added are described in the VCF header.</p><p>For GFF and GTF files, the gene models are treated the same as other gene models loaded from the cache or database, so are used to calculate consequences etc and will result in a full “block” of annotation in the VCF output for each overlapped transcript. No specific fields are added other than the SOURCE field being set to the short name (or filename).</p><p>For BED and bigWig files, only one field is added. For bigWig this is the recorded score at that position. For BED this will be either the 4th column of the BED (usually some sort of ID), or if this is absent (or the report_coords flag is set), the coordinates of the feature.</p><p>For VCF files, the minimal behaviour is similar to BED, but users may optionally request additional fields from the VCF INFO field to be reported. These are, if available in this format, reported in an allele-specific manner. This allows, for example, VEP to get per-allele frequency data from gnomAD VCF files.</p><p>Hope that helps!</p><p>Will McLaren</p><p>Ensembl Variation</p><div><blockquote type="cite" class="clean_bq" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"><span><div><div><br><br>Thank You All<span class="Apple-converted-space"> </span><br><br>very nice tool, VEP!<span class="Apple-converted-space"> </span><br><br><br>Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. 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