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<p>I've been running the new VEP package on the v87 GRCh37 downloaded cache, and get a warning for just one of the lines in my input VCF.</p>
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<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">20<span style="white-space: pre;">
</span>34067454<span style="white-space: pre;"> </span>.<span style="white-space: pre;">
</span>AT<span style="white-space: pre;"> </span>A</span></p>
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<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">WARNING: 63631 : Use of uninitialized value $cdna_position in pattern match (m//) at /exports/igmm/software/pkg/el7/libs/ensembl_api/85/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
line 1901, <GEN4> line 57651.</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">Use of uninitialized value $cdna_coord in concatenation (.) or string at /exports/igmm/software/pkg/el7/libs/ensembl_api/85/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
line 1933, <GEN4> line 57651.</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">Use of uninitialized value $exon_start_coord in addition (+) at /exports/igmm/software/pkg/el7/libs/ensembl_api/85/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 703,
<GEN4> line 57651.</span></p>
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<p>When I try inputting this variant to the GRCh37 web interface, it works. I also didn't get any warnings when running the old VEP package on the v86 GRCh37 downloaded cache, and get the following hits:</p>
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<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">ENSG00000126001<span style="white-space: pre;">
</span>ENST00000342580<span style="white-space: pre;"> </span>intron_variant</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">ENSG00000126001<span style="white-space: pre;">
</span>ENST00000397527<span style="white-space: pre;"> </span>intron_variant</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">ENSG00000126001</span><span style="font-variant-ligatures: no-common-ligatures; white-space: pre;">
</span><span style="font-variant-ligatures: no-common-ligatures;">ENST00000425096</span><span style="font-variant-ligatures: no-common-ligatures; white-space: pre;">
</span><span style="font-variant-ligatures: no-common-ligatures;">downstream_gene_variant</span><br>
</p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">ENSG00000126001<span style="white-space: pre;">
</span>ENST00000425934<span style="white-space: pre;"> </span>downstream_gene_variant</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;"></p>
<p style="margin-right: 0px; margin-left: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;"><span style="font-family: Menlo; font-size: 11px; font-variant-ligatures: no-common-ligatures;">ENSG00000126001</span><span style="font-family: Menlo; font-size: 11px; font-variant-ligatures: no-common-ligatures; white-space: pre;">
</span><span style="font-family: Menlo; font-size: 11px; font-variant-ligatures: no-common-ligatures;">ENST00000461386</span><span style="font-family: Menlo; font-size: 11px; font-variant-ligatures: no-common-ligatures; white-space: pre;">
</span><span style="font-family: Menlo; font-size: 11px; font-variant-ligatures: no-common-ligatures;">downstream_gene_variant</span></p>
<div>ENSG00000230155<span style="white-space: pre;"> </span>ENST00000416260<span style="white-space: pre;">
</span>intron_variant,non_coding_transcript_variant<br>
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<div>ENSG00000230155<span style="white-space: pre;"> </span>ENST00000444933<span style="white-space: pre;">
</span>intron_variant,non_coding_transcript_variant<br>
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<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">ENSG00000230155<span style="white-space: pre;">
</span>ENST00000453914<span style="white-space: pre;"> </span>intron_variant,non_coding_transcript_variant</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
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<p><span style="font-size: 12pt;">Cheers,</span><br>
</p>
<p>Alison</p>
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