<div dir="ltr">Bug is fixed on release/76 branch of ensembl-variation now anyway.<div><br></div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 26 August 2014 14:33, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br>
<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>Thanks for spotting that, definitely a bug.</div><div><br></div><div>You can have the VEP keep the original CSQ field using --keep_csq which sort of bypasses the problem, though I'm not sure if the resulting VCF with two CSQ entries violates VCF spec.</div>

<div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div class="h5">On 26 August 2014 14:22, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span> wrote:<br>

</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><u></u>
<div>
<span><div>Hi dev team,</div>
<div><br></div>
<div>I've run into what appears to be a bug in VEP. If you already have a CSQ field in a VCF, VEP is supposed to overwrite it (which it does properly). However, I ran into the case where I had an old CSQ field (that I wanted to update) followed by additional fields, and VEP appears to delete these additional fields! (Additionally, it seems to introduce an additional semicolon sometimes, but that's obviously not as big a deal). Example VCF:</div>


<div><br></div>
<div>
<div>1       739142  rs2340527       T       A       1        PASS    AC=5;CSQ=||||;AN=100</div>
<br>
</div>
<div>results in:</div>
<div><br></div>
<div>
<div>1       739142  rs2340527       T       A       1       PASS    AC=5;;CSQ=A|ENSG00000237491|ENST00000588951|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||1/3||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000237491|ENST00000429505|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||1/2||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000237491|ENST00000591440|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||1/2||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000237491|ENST00000590848|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||3/4||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000237491|ENST00000589531|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||1/3||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000230092|ENST00000590817|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||3/3||||||-1|||RP11-206L10.8|Clone_based_vega_gene|||-:0.0303|transcribed_unprocessed_pseudogene||||||||||||,A|ENSG00000237491|ENST00000586288|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||4/6||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000237491|ENST00000587530|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||2/3||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000230092|ENST00000447500|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||3/3||||||-1||YES|RP11-206L10.8|Clone_based_vega_gene|||-:0.0303|processed_transcript||||||||||||,A|ENSG00000237491|ENST00000593022|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||1/3||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||</div>


<br>
</div>
<div>and AN=100 is nowhere to be found.</div>
<div><br></div>
<div>-Konrad</div></span><span><font color="#888888"><div>-Konrad</div>
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