<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hello!<div class=""><br class=""></div><div class="">Yes, I figured I could do by going into the API (with VEP, that would involve writing a plugin), but thought maybe it's already implemented in native VEP.</div><div class=""><br class=""></div><div class="">In any case, I found a partial solution, the --hgvs flag appears to write out the version number for transcripts (e.g. ENST00000302118.5:c.-26G>A), which is most of what I need (though it doesn't have this for genes). <br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class="Apple-interchange-newline">-Konrad</div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Jan 9, 2015, at 2:10 AM, Rocky Bernstein <<a href="mailto:rocky.bernstein@gmail.com" class="">rocky.bernstein@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Comment in line.<br class=""><div class=""><br class=""><div class="gmail_extra"><br class=""><div class="gmail_quote">On Thu, Jan 8, 2015 at 4:47 PM, Konrad Karczewski <span dir="ltr" class=""><<a href="mailto:konradk@broadinstitute.org" target="_blank" class="">konradk@broadinstitute.org</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><u class=""></u>
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<span class=""><div class="">Hi VEP team/Will,</div>
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<div class="">In some applications, Ensembl Gene IDs have a version number (i.e. ENSG00000000001.2) - is there a way I can get this information from a particular run of VEP? Or at least figure out which particular version of each gene I have in a cache?</div></span></div></blockquote><div class=""><br class=""></div><div class="">I know very little about VEP, and am not sure I even totally understand what you are asking. However since half of the VEP team is out until the end of the month, I'll give it a shot; I can read a manual page. The following code is pretty much straight out of man Bio::DB::Fasta: <span style="font-family:monospace,monospace" class=""><br class=""><br class=""></span><span style="font-family:monospace,monospace" class=""><span style="font-family:monospace,monospace" class="">use Bio::DB::Fasta;<br class="">my $fasta_file = glob('~/.vep/homo_sapiens/78_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa');<br class="">my $db = Bio::DB::Fasta->new($fasta_file);<br class=""></span>my @ids = $db->get_all_primary_ids;<br class="">print join(', ', @ids, "\n");<br class=""></span><span style="font-family:arial,helvetica,sans-serif" class=""><br class=""></span></div><div class=""><span style="font-family:arial,helvetica,sans-serif" class="">If you aren't using Fasta, them I imagine you if read the man page for whatever DB you are using , it probably has $db->get_all_primary_id . <br class=""><br class=""></span></div><div class=""><span style="font-family:arial,helvetica,sans-serif" class="">If you are referring to your input VCF file instead, I don't know.</span><span style="font-family:monospace,monospace" class=""><br class=""><br class=""></span></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class=""><span class="">
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<div class="">Thanks!</div></span><div class=""><br class=""></div>
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