<span id="mailbox-conversation"><div>Hi Will,</div>
<div><br></div>
<div>Thanks! Looks like the BioPerl update actually was the culprit. All set now, thanks!</div></span><div class="mailbox_signature"><br></div>
<br><br><div class="gmail_quote"><p>On Fri, Nov 21, 2014 at 4:22 AM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br></p><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div dir="ltr">Hi Konrad,<div><br></div>
<div>I can't recreate this issue, but my guess would be it's some combination of incorrect assembly or FASTA file. Without knowing what setup you're using it's hard for me to say exactly what.</div>
<div><br></div>
<div>If I run the following skeleton plugin:</div>
<div><br></div>
<div>
<div>package Skeleton;</div>
<div>use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;</div>
<div>use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);</div>
<div><br></div>
<div>sub run {</div>
<div>  my ($self, $tva) = @_;</div>
<div>  print STDERR "Sequence ".$tva->variation_feature->feature_Slice->expand(1, 1)->seq."\n";</div>
<div>  return {};</div>
<div>}</div>
<div><br></div>
<div>1;</div>
</div>
<div><br></div>
<div>I get the same results using 75, 76 and 77, using either --database or --cache with a FASTA file:</div>
<div><br></div>
<div>
<div>2014-11-21 09:19:35 - Read existing cache info</div>
<div>2014-11-21 09:19:35 - Auto-detected FASTA file in cache directory</div>
<div>2014-11-21 09:19:35 - Checking/creating FASTA index</div>
<div>2014-11-21 09:19:35 - Loaded plugin: Skeleton</div>
<div>2014-11-21 09:19:35 - Starting...</div>
<div>2014-11-21 09:19:35 - Detected format of input file as vcf</div>
<div>2014-11-21 09:19:35 - Read 1 variants into buffer</div>
<div>2014-11-21 09:19:35 - Reading transcript data from cache and/or database</div>
<div>[==========]  [ 100% ]</div>
<div>2014-11-21 09:19:35 - Retrieved 185 transcripts (0 mem, 185 cached, 0 DB, 0 duplicates)</div>
<div>2014-11-21 09:19:35 - Analyzing chromosome 1</div>
<div>2014-11-21 09:19:35 - Analyzing variants</div>
<div>[==========]  [ 100% ]</div>
<div>2014-11-21 09:19:35 - Calculating consequences</div>
<div>Sequence GCA</div>
<div>Sequence GCA</div>
<div>...etc...<br></div>
</div>
<div><br></div>
<div>If using a FASTA file, double check the assembly matches that of your cache, and re-generate the index. There are also known issues with older version of BioPerl re: the FASTA indexing - make sure that you are using an up to date (>1.6) version of BioPerl.</div>
<div><br></div>
<div>Regards</div>
<div><br></div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra">
<br><div class="gmail_quote">On 20 November 2014 21:06, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org">konradk@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi dev team,<div><br></div>
<div>I've run into a strange issue when comparing output from v75 and v77. I'm looking to get 1 base context around a variant, which I've gotten using:</div>
<div><br></div>
<div>$transcript_variation_allele->variation_feature->feature_Slice->expand(1, 1)->seq;</div>
<div><br></div>
<div>When running this on a synthetic variant:</div>
<div><br></div>
<div>1       12141   .       C       A,T,G   .       .</div>
<div><br></div>
<div>I get the expected result in v75 (note that context 1 bp around the variant is GCA as such: <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:12140-12142">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A12140-12142</a>)</div>
<div><br></div>
<div>CSQ=A|ENSG00000223972|ENST00000456328|Transcript|non_coding_exon_variant&nc_transcript_variant|273||||||||1|1/3|||||||1||YES|DDX11L1|HGNC||||processed_transcript||||ENST00000456328.2:n.273C>A|||||||||||GCA,T|ENSG00000223972|ENST00000456328|Transcript|non_coding_exon_variant&nc_transcript_variant|273||||||||2|1/3|||||||1||YES|DDX11L1|HGNC||||processed_transcript||||ENST00000456328.2:n.273C>T|||||||||||GCA,G|ENSG00000223972|ENST00000456328|Transcript|non_coding_exon_variant&nc_transcript_variant|273||||||||3|1/3|||||||1||YES|DDX11L1|HGNC||||processed_transcript||||ENST00000456328.2:n.273C>G|||||||||||GCA,A|ENSG00000223972|ENST00000450305|Transcript|intron_variant&nc_transcript_variant|||||||||1||1/5||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000450305.2:n.49-38C>A|||||||||||GCA,T|ENSG00000223972|ENST00000450305|Transcript|intron_variant&nc_transcript_variant|||||||||2||1/5||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000450305.2:n.49-38C>T|||||||||||GCA,G|ENSG00000223972|ENST00000450305|Transcript|intron_variant&nc_transcript_variant|||||||||3||1/5||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000450305.2:n.49-38C>G|||||||||||GCA,A|ENSG00000223972|ENST00000515242|Transcript|non_coding_exon_variant&nc_transcript_variant|270||||||||1|1/3|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000515242.2:n.270C>A|||||||||||GCA,T|ENSG00000223972|ENST00000515242|Transcript|non_coding_exon_variant&nc_transcript_variant|270||||||||2|1/3|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000515242.2:n.270C>T|||||||||||GCA,G|ENSG00000223972|ENST00000515242|Transcript|non_coding_exon_variant&nc_transcript_variant|270||||||||3|1/3|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000515242.2:n.270C>G|||||||||||GCA,A|ENSG00000223972|ENST00000518655|Transcript|non_coding_exon_variant&nc_transcript_variant|268||||||||1|1/4|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000518655.2:n.268C>A|||||||||||GCA,T|ENSG00000223972|ENST00000518655|Transcript|non_coding_exon_variant&nc_transcript_variant|268||||||||2|1/4|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000518655.2:n.268C>T|||||||||||GCA,G|ENSG00000223972|ENST00000518655|Transcript|non_coding_exon_variant&nc_transcript_variant|268||||||||3|1/4|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000518655.2:n.268C>G|||||||||||GCA</div>
<div><br></div>
<div>but same command/code running under VEP v77, I get this:</div>
<div><br></div>
<div>CSQ=A|ENSG00000223972|ENST00000456328|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|273||||||1||1|DDX11L1|HGNC||processed_transcript|YES||||||||1/3|||ENST00000456328.2:n.273G>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000456328|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|273||||||2||1|DDX11L1|HGNC||processed_transcript|YES||||||||1/3|||ENST00000456328.2:n.273G>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000456328|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|273||||||3||1|DDX11L1|HGNC||processed_transcript|YES||||||||1/3|||||||||||||||||||||||CTT,A|ENSG00000223972|ENST00000450305|Transcript|intron_variant&non_coding_transcript_variant|||||||1||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene||||||||||1/5||ENST00000450305.2:n.49-38C>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000450305|Transcript|intron_variant&non_coding_transcript_variant|||||||2||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene||||||||||1/5||ENST00000450305.2:n.49-38C>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000450305|Transcript|intron_variant&non_coding_transcript_variant|||||||3||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene||||||||||1/5||ENST00000450305.2:n.49-38C>G||||||||||||||||||||CTT,A|ENSG00000223972|ENST00000515242|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|270||||||1||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/3|||ENST00000515242.2:n.270G>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000515242|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|270||||||2||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/3|||ENST00000515242.2:n.270G>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000515242|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|270||||||3||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/3|||||||||||||||||||||||CTT,A|ENSG00000223972|ENST00000518655|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|268||||||1||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/4|||ENST00000518655.2:n.268G>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000518655|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|268||||||2||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/4|||ENST00000518655.2:n.268G>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000518655|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|268||||||3||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/4|||||||||||||||||||||||CTT</div>
<div><br></div>
<div>Any ideas why this might be the case? Happy to send the plugin and command line prompts if that would be helpful.<br><div><br></div>
<div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Thanks!<span class="HOEnZb"><font color="#888888"><br>-Konrad</font></span>
</div></div>
</div>
<br></div>
</div>
<br>_______________________________________________<br>
Dev mailing list    <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br><br></blockquote>
</div>
<br></div>
</blockquote></div><br>