[ensembl-dev] Feature slice issue

Fri Nov 21 21:31:44 GMT 2014

Hi Will,

Thanks! Looks like the BioPerl update actually was the culprit. All set now, thanks!

On Fri, Nov 21, 2014 at 4:22 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Konrad,
> I can't recreate this issue, but my guess would be it's some combination of
> incorrect assembly or FASTA file. Without knowing what setup you're using
> it's hard for me to say exactly what.
> If I run the following skeleton plugin:
> package Skeleton;
> use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
> use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
> sub run {
>   my ($self, $tva) = @_;
>   print STDERR "Sequence
> ".$tva->variation_feature->feature_Slice->expand(1, 1)->seq."\n";
>   return {};
> }
> 1;
> I get the same results using 75, 76 and 77, using either --database or
> --cache with a FASTA file:
> 2014-11-21 09:19:35 - Read existing cache info
> 2014-11-21 09:19:35 - Auto-detected FASTA file in cache directory
> 2014-11-21 09:19:35 - Checking/creating FASTA index
> 2014-11-21 09:19:35 - Loaded plugin: Skeleton
> 2014-11-21 09:19:35 - Starting...
> 2014-11-21 09:19:35 - Detected format of input file as vcf
> 2014-11-21 09:19:35 - Read 1 variants into buffer
> 2014-11-21 09:19:35 - Reading transcript data from cache and/or database
> [==========]  [ 100% ]
> 2014-11-21 09:19:35 - Retrieved 185 transcripts (0 mem, 185 cached, 0 DB, 0
> duplicates)
> 2014-11-21 09:19:35 - Analyzing chromosome 1
> 2014-11-21 09:19:35 - Analyzing variants
> [==========]  [ 100% ]
> 2014-11-21 09:19:35 - Calculating consequences
> Sequence GCA
> Sequence GCA
> ...etc...
> If using a FASTA file, double check the assembly matches that of your
> cache, and re-generate the index. There are also known issues with older
> version of BioPerl re: the FASTA indexing - make sure that you are using an
> up to date (>1.6) version of BioPerl.
> Regards
> Will McLaren
> Ensembl Variation
> On 20 November 2014 21:06, Konrad Karczewski <konradk at broadinstitute.org>
> wrote:
>> 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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>>
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