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<span id="mailbox-conversation"><div>Hi dev team,</div>
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<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>
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<div>1 739142 rs2340527 T A 1 PASS AC=5;CSQ=||||;AN=100</div>
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<div>results in:</div>
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<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>
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<div>and AN=100 is nowhere to be found.</div>
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<div>-Konrad</div></span><div class="mailbox_signature">-Konrad</div>
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