<div dir="ltr">Hi Konrad,<div><br></div><div>Thanks for the bug report.</div><div><br></div><div>A bizarre one-in-a-million chance meant that the regulatory feature in question was getting discarded due to a clash of internal identifiers. This is now fixed on release/79 and release/80.</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 26 May 2015 at 04:58, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">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 Will, dev team,<div><br></div><div>I've found what is appearing to be a strange issue (I always seem to find these corner cases) in VEP. Running the same VEP command twice on two files, one with ~1K variants (spanning all 22 chromosomes), and one with a single variant (that is included in the first file) appears to give a different result in the two runs for regulatory_region_variant annotations.</div><div><br></div><div>The two annotated files are available at <a href="http://www.broadinstitute.org/~konradk/vep/" target="_blank">http://www.broadinstitute.org/~konradk/vep/</a></div><div><br></div><div>Command line call in both cases (minus input filename):</div><div><br></div><div>perl /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --everything --vcf --allele_number --no_stats --cache --offline --dir /humgen/atgu1/fs03/konradk/vep/gold/ --force_overwrite --cache_version 79 --fasta /tmp/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --assembly GRCh37 --tabix --plugin LoF,human_ancestor_fa:/humgen/atgu1/fs03/konradk/loftee_data//human_ancestor.fa.gz,filter_position:0.05,min_intron_size:15,conservation_file:mysql -i /humgen/atgu1/fs03/konradk/lof/exac_subset.vcf.gz -o /humgen/atgu1/fs03/konradk/lof/exac_subset.vep.vcf.gz</div><div><br></div><div>In both cases, it appears to have loaded the regulatory features, but then returns different results.</div><div><br></div><div>Variant when run in a larger set:</div><div><br></div><div><div>2015-05-25 22:40:17 - Retrieved 369524 regulatory features (0 mem, 395468 cached, 0 DB, 25944 duplicates)</div></div><div><br></div><div>1<span style="white-space:pre-wrap"> </span>78340517<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>C<span style="white-space:pre-wrap"> </span>652.97<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>CSQ=C|intron_variant|MODIFIER|FAM73A|ENSG00000180488|Transcript|ENST00000443751|protein_coding||14/14|ENST00000443751.2:c.1570-14T>C|||||||rs540912776|1||1|HGNC|24741||||ENSP00000393675||F8W7S1_HUMAN|UPI000206500B|||||||||||||||||||||||,C|intron_variant|MODIFIER|FAM73A|ENSG00000180488|Transcript|ENST00000370791|protein_coding||15/15|ENST00000370791.3:c.1681-14T>C|||||||rs540912776|1||1|HGNC|24741|YES||CCDS681.1|ENSP00000359827|FA73A_HUMAN|R4GMP2_HUMAN&B7ZLZ8_HUMAN|UPI00000722C6|||||||||||||||||||||||</div><div>
<br></div><div>Variant when run on its own:</div><div><br></div><div><div>2015-05-25 22:49:19 - Retrieved 372 regulatory features (0 mem, 372 cached, 0 DB, 0 duplicates)</div><div><br></div></div><div>1 78340517 . T C 652.97 PASS CSQ=C|intron_variant|MODIFIER|FAM73A|ENSG00000180488|Transcript|ENST00000443751|protein_coding||14/14|ENST00000443751.2:c.1570-14T>C|||||||rs540912776|1||1|HGNC|24741||||ENSP00000393675||F8W7S1_HUMAN|UPI000206500B|||||||||||||||||||||||,C|intron_variant|MODIFIER|FAM73A|ENSG00000180488|Transcript|ENST00000370791|protein_coding||15/15|ENST00000370791.3:c.1681-14T>C|||||||rs540912776|1||1|HGNC|24741|YES||CCDS681.1|ENSP00000359827|FA73A_HUMAN|R4GMP2_HUMAN&B7ZLZ8_HUMAN|UPI00000722C6|||||||||||||||||||||||,C|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000539328|promoter_flanking_region||||||||||rs540912776|1||||||||||||||||||||||||||||||||||</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>-Konrad</div></font></span></div><br>_______________________________________________<br>
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<br></blockquote></div><br></div>