[ensembl-dev] Feature slice issue

Konrad Karczewski konradk at broadinstitute.org
Thu Nov 20 21:06:30 GMT 2014


Hi dev team,

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:

$transcript_variation_allele->variation_feature->feature_Slice->expand(1, 1)->seq;

When running this on a synthetic variant:

1       12141   .       C       A,T,G   .       .

I get the expected result in v75 (note that context 1 bp around the variant is GCA as such: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A12140-12142 <http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:12140-12142>)

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

but same command/code running under VEP v77, I get this:

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

Any ideas why this might be the case? Happy to send the plugin and command line prompts if that would be helpful.

Thanks!
-Konrad

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