[ensembl-dev] UpDownDistance using
Will McLaren
wm2 at ebi.ac.uk
Mon Jun 2 14:18:09 BST 2014
I think if I were presented with this issue I would be going about it in a
different way.
If your goal is to find all genes within a set of genomic intervals (as
defined by the variants and the required up/downstream distance), you'd be
better off downloading a list of the genes and their coordinates and
writing a short script or bend some piece of software to find the overlaps
between your search areas and the genes.
The quickest way I can think to do this off the top of my head is to use
something like a tabix-indexed BED or GTF file of genes, then do a tabix
lookup on this file for each of your intervals.
Trying to bend the VEP to do this is in my opinion a bit overkill, as all
the VEP will be calling for each of those genes is e.g.
upstream_gene_variant.
Will
On 2 June 2014 13:44, Genomeo Dev <genomeodev at gmail.com> wrote:
> Thanks Will. Yes that is what I want to achieve. Given so much variant
> data is coming out of GWAS studies, because of LD structure the approach
> of considering specific loci for variant analysis is becoming increasingly
> common.
>
> I have tried to write an individual input file for VEP for each variant
> but since they are in the rank of 100K this is very slow to run. I don't
> know how easy would be to adjust the VEP API to take in a fixed range of
> coordinates as well as the relative upstream and downstream coordinates.
> This way, I could set the fixed limits up in a new() method and VEP would
> process all the variants at once.
>
>
> Thanks,
>
> G.
>
>
> On 2 June 2014 13:24, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
>> Hello again,
>>
>> I think I'm getting a little lost here with exactly what you're trying to
>> do with the plugin.
>>
>> If I understand correctly, you are trying to adjust the upstream and
>> downstream search distance on a per-variant basis? e.g. use 5kb for
>> variant1, 10kb for variant2?
>>
>> This is not possible using a plugin currently as the plugin code in the
>> run() method is executed after the transcripts are found and the
>> consequences are called. It is possible to set it globally, as in the
>> UpDownDistance plugin, as this is done in the new() method which is
>> executed once when the script starts up.
>>
>> I think the only way to achieve this would be to group your variants into
>> different input files by the distance cutoff required, and run them as
>> separate VEP commands with different distances passed to the UpDownDistance
>> plugin.
>>
>> HTH
>>
>> Will
>>
>>
>>
>>
>> On 2 June 2014 09:34, Genomeo Dev <genomeodev at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> With regard to to the question with the aim to specify UPSTREAM_DISTANCE
>>> and DOWNSTREAM_DISTANCE limits for each variant in an input list of
>>> variants, if it is not possible to achieve that because of how VEP
>>> interacts with plug-ins, would it be possible to introduce UPSTREAM_COORDINATE
>>> and DOWNSTREAM_COORDINATE variables declarable within a plugin which
>>> would then allow to restrict where VEP looks for consequences?
>>>
>>> Regards,
>>>
>>> G.
>>>
>>>
>>>
>>> On 30 May 2014 17:49, Genomeo Dev <genomeodev at gmail.com> wrote:
>>>
>>>> I did eventually figure out the answer to the first question: my
>>>> ($self, $tva) = @_; $self->params()
>>>>
>>>> For my second question, more specifically, what I want to do is to be
>>>> able to use the original input coordinate for each individual input variant
>>>> to then specify the UPSTREAM_DISTANCE and DOWNSTREAM_DISTANCE limits
>>>> per variant in UpDownDistance.pm. The reason for that is I have a
>>>> large group of variants for which I want to consider consequences within
>>>> the same physical range which I can already pass on the the plugin as
>>>> arguments. Running VEP per variant is not efficient hence the question.
>>>>
>>>> Regards,
>>>>
>>>> G.
>>>>
>>>>
>>>> On 30 May 2014 15:48, Genomeo Dev <genomeodev at gmail.com> wrote:
>>>>
>>>>> A related question is where how to get the inputed variant attributes
>>>>> (e.g. position, reference ID) so to process that within the subroutine.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> G.
>>>>>
>>>>>
>>>>> On 30 May 2014 13:01, Genomeo Dev <genomeodev at gmail.com> wrote:
>>>>>
>>>>>> Thanks Will. It is working fine now.
>>>>>>
>>>>>> I wanted to modify the UpDownDistance.pm to produce two separate
>>>>>> columns in the VEP output showing the UPDIST_CUTOFF and UPDIST_CUTOFF
>>>>>> parameters (See below). Please how do I fetch the plugin arguments into the
>>>>>> run subroutine?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> G.
>>>>>>
>>>>>>
>>>>>> use strict;
>>>>>> use warnings;
>>>>>> use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
>>>>>>
>>>>>> sub feature_types {
>>>>>> return ['Feature', 'Intergenic'];
>>>>>> }
>>>>>>
>>>>>> sub get_header_info {
>>>>>> return {
>>>>>> UPDIST_CUTOFF => "distance cutoff upstream variant where
>>>>>> consequences are calculated",
>>>>>> DOWNIDST_CUTOFF => "distance cutoff downstream variant where
>>>>>> consequences are calculated"
>>>>>> };
>>>>>> }
>>>>>>
>>>>>> sub new {
>>>>>>
>>>>>> my $class = shift;
>>>>>> my $self = $class->SUPER::new(@_);
>>>>>>
>>>>>> # change up/down
>>>>>> my $up = $self->params->[0] || 5000;
>>>>>>
>>>>>> my $down = $self->params->[1] || $up;
>>>>>>
>>>>>> $Bio::EnsEMBL::Variation::Utils::VariationEffect::UPSTREAM_DISTANCE = $up;
>>>>>>
>>>>>> $Bio::EnsEMBL::Variation::Utils::VariationEffect::DOWNSTREAM_DISTANCE =
>>>>>> $down;
>>>>>>
>>>>>> return $self;
>>>>>>
>>>>>> }
>>>>>>
>>>>>>
>>>>>> sub run {
>>>>>> my $upstream_distance = ?
>>>>>> my $downstream_distance = ?
>>>>>> return {
>>>>>> UPDIST_CUTOFF => $upstream_distance,
>>>>>> DOWNDIST_CUTOFF => $downstream_distance
>>>>>> }
>>>>>> };
>>>>>>
>>>>>> 1;
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 29 May 2014 09:57, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I've patched a fix in for the UpDownDistance issue, the fix is in
>>>>>>> the main ensembl-variation API.
>>>>>>>
>>>>>>> Regarding the DISTANCE field, perhaps you could write a plugin that
>>>>>>> does exactly what you want? Changing the behaviour of this field may not be
>>>>>>> compatible with other people's pipelines, and the plugin system is the
>>>>>>> perfect way for you to have annotations customised to your requirements.
>>>>>>>
>>>>>>> Regards
>>>>>>>
>>>>>>> Will
>>>>>>>
>>>>>>>
>>>>>>> On 28 May 2014 18:58, Genomeo Dev <genomeodev at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> When using different up and down arguments in UpDownDistance.pm,
>>>>>>>> VEP returns genes outside the specified range as shown in the example below
>>>>>>>> (MIR1302-4 is 94161 upstream of rs17808606 but is still reported
>>>>>>>> using UpDownDistance,5000,100000). For the genes which are outside
>>>>>>>> the range, the DISTANCE and Consequence columns are empty while for example
>>>>>>>> TSSDistance is not empty which might indicate the up and down arguments may
>>>>>>>> not be processed correctly.
>>>>>>>>
>>>>>>>> It would be helpful to only return genes whose coordinates satisfy
>>>>>>>> the specified range. Also, it would immensely help as well if DISTANCE is
>>>>>>>> set to 0 for variants falling within genes and is otherwise calculated even
>>>>>>>> for non-transcript feature types.
>>>>>>>>
>>>>>>>> Note that I am using Ensembl 75 updated with the recently updated
>>>>>>>> ensembl variantion module which allowed UpDownDistance.pm to work for
>>>>>>>> distances beyond 5kb.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> G.
>>>>>>>>
>>>>>>>> ##UpDownDistance,5000,100000
>>>>>>>> ##TSSDistance
>>>>>>>> #Uploaded_variation Location Allele Existing_variation
>>>>>>>> SYMBOL SYMBOL_SOURCE Gene ENSP Feature Feature_type BIOTYPE STRAND
>>>>>>>> CANONICAL EXON INTRON DISTANCE TSSDistance Consequence rs17808606
>>>>>>>> 2:208228309 T rs17808606 AC007879.5 Clone_based_vega_gene
>>>>>>>> ENSG00000223725 - ENST00000412387 Transcript antisense -1 - - 3/4 -
>>>>>>>> - intron_variant,nc_transcript_variant rs17808606 2:208228309 T
>>>>>>>> rs17808606 MIR1302-4 HGNC ENSG00000221628 - ENST00000408701
>>>>>>>> Transcript miRNA -1 YES - - - 94161 rs17808606 2:208228309 T
>>>>>>>> rs17808606 AC007879.6 Clone_based_vega_gene ENSG00000225064 -
>>>>>>>> ENST00000438824 Transcript lincRNA 1 YES - - 92895 -
>>>>>>>> downstream_gene_variant rs17808606 2:208228309 T rs17808606
>>>>>>>> AC007879.5 Clone_based_vega_gene ENSG00000223725 - ENST00000418850
>>>>>>>> Transcript antisense -1 YES - 4/5 - -
>>>>>>>> intron_variant,nc_transcript_variant
>>>>>>>> ##UpDownDistance,100000
>>>>>>>> ##TSSDistance
>>>>>>>> #Uploaded_variation Location Allele Existing_variation SYMBOL
>>>>>>>> SYMBOL_SOURCE Gene ENSP Feature Feature_type BIOTYPE STRAND
>>>>>>>> CANONICAL EXON INTRON DISTANCE TSSDistance Consequence rs17808606
>>>>>>>> 2:208228309 T rs17808606 AC007879.5 Clone_based_vega_gene
>>>>>>>> ENSG00000223725 - ENST00000412387 Transcript antisense -1 - - 3/4 -
>>>>>>>> - intron_variant,nc_transcript_variant rs17808606 2:208228309 T
>>>>>>>> rs17808606 MIR1302-4 HGNC ENSG00000221628 - ENST00000408701
>>>>>>>> Transcript miRNA -1 YES - - 94161 94161 upstream_gene_variant
>>>>>>>> rs17808606 2:208228309 T rs17808606 AC007879.6
>>>>>>>> Clone_based_vega_gene ENSG00000225064 - ENST00000438824 Transcript
>>>>>>>> lincRNA 1 YES - - 92895 - downstream_gene_variant rs17808606
>>>>>>>> 2:208228309 T rs17808606 AC007879.5 Clone_based_vega_gene
>>>>>>>> ENSG00000223725 - ENST00000418850 Transcript antisense -1 YES - 4/5
>>>>>>>> - - intron_variant,nc_transcript_variant
>>>>>>>>
>>>>>>>>
>>>>>>>> On 27 May 2014 11:03, Genomeo Dev <genomeodev at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Sorry seems the plug-in already does that thanks!
>>>>>>>>>
>>>>>>>>> G.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 23 May 2014 19:14, Genomeo Dev <genomeodev at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Will,
>>>>>>>>>>
>>>>>>>>>> Thanks very much. That worked nicely.
>>>>>>>>>>
>>>>>>>>>> I am working with a set of variants within a locus where I know
>>>>>>>>>> that they are LD-independent with other genes from outside this locus.
>>>>>>>>>> Therefore, I want only to focus on genes inside this physically defined
>>>>>>>>>> locus.
>>>>>>>>>>
>>>>>>>>>> Rarely do these variants fall exactly at the centre of the locus
>>>>>>>>>> so distances to the right and left boundaries are not equal. Would it be
>>>>>>>>>> possible to alter UpDownDistance.pm to be able to specify a
>>>>>>>>>> start and end coordinate within which VEP should be constrained instead of
>>>>>>>>>> the current distance cutoff?
>>>>>>>>>>
>>>>>>>>>> Many thanks,
>>>>>>>>>>
>>>>>>>>>> G.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 8 May 2014 16:12, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hello again,
>>>>>>>>>>>
>>>>>>>>>>> I've fixed a bug that prevented UpDownDistance functioning
>>>>>>>>>>> correctly - it hadn't been tested with larger distances such as you
>>>>>>>>>>> specified which broke some assumptions in the core VEP code.
>>>>>>>>>>> You will need to update your ensembl-variation module or re-run
>>>>>>>>>>> the VEP INSTALL.pl script to pick up the new API code.
>>>>>>>>>>>
>>>>>>>>>>> As far as the other plugins go, I think you are misunderstanding
>>>>>>>>>>> how some of them work:
>>>>>>>>>>>
>>>>>>>>>>> TSSDistance - this gives the distance between a variant and the
>>>>>>>>>>> annotated transcript start site. If a variant is annotated as intergenic,
>>>>>>>>>>> there is no transcript to give the distance to! Changing the code to force
>>>>>>>>>>> it to assess intergenic variants will of course break here. Of course if
>>>>>>>>>>> you alter the up/down-stream distance using UpDownStream such that this
>>>>>>>>>>> then finds a transcript in range, the plugin will then work as expected
>>>>>>>>>>> without modification. It seems to me that you are expecting that this
>>>>>>>>>>> plugin will find the shortest distance to _any_ transcript start site,
>>>>>>>>>>> which is not the intended purpose of the code.
>>>>>>>>>>>
>>>>>>>>>>> Condel & dbNSFP - these two plugins work exclusively on missense
>>>>>>>>>>> AKA non-synonymous SNVs (hence the NS in the name dbNSFP). While dbNSFP
>>>>>>>>>>> carries scores for CADD, and CADD gives scores for any genomic position,
>>>>>>>>>>> the CADD scores in dbNSFP are only for missense variants.
>>>>>>>>>>>
>>>>>>>>>>> The feature_types() subroutine should be used when writing your
>>>>>>>>>>> own plugin to determine which kind of variant/feature combinations are
>>>>>>>>>>> considered by the plugin, since the run() sub is executed once for each
>>>>>>>>>>> variant/feature overlap found by the core VEP code. Modifying existing
>>>>>>>>>>> plugins like this should be done only if you are confident that the
>>>>>>>>>>> modification achieves what you intend.
>>>>>>>>>>>
>>>>>>>>>>> Hope that all helps
>>>>>>>>>>>
>>>>>>>>>>> Will
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 7 May 2014 17:59, Genomeo Dev <genomeodev at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Thanks Will.
>>>>>>>>>>>>
>>>>>>>>>>>> I am working with non-coding and intergenic variants and wanted
>>>>>>>>>>>> to run VEP with the following plugins:
>>>>>>>>>>>>
>>>>>>>>>>>> --plugin UpDownDistance,100000 \
>>>>>>>>>>>> --plugin TSSDistance \
>>>>>>>>>>>> --plugin
>>>>>>>>>>>> Condel,/media/sf_D_DRIVE/Projects/Databases/ensembl/Plugins/Condel/config,b
>>>>>>>>>>>> \
>>>>>>>>>>>> --plugin
>>>>>>>>>>>> CADD,/media/sf_D_DRIVE/Projects/Databases/CADD/v1.0/1000G.tsv.gz \
>>>>>>>>>>>> --plugin
>>>>>>>>>>>> Gwava,tss,/media/sf_D_DRIVE/Projects/Databases/gwava/gwava_scores.bed.gz \
>>>>>>>>>>>> --plugin Conservation,GERP_CONSERVATION_SCORE,mammals \
>>>>>>>>>>>> --plugin
>>>>>>>>>>>> dbNSFP,/media/sf/data/dbNSFP/dbNSFP2.4.gz,GERP++_NR,GERP++_RS,LRT_score,LRT_pred,MutationTaster_score,MutationTaster_pred,MutationAssessor_score,MutationAssessor_pred,FATHMM_score,FATHMM_pred,RadialSVM_score,RadialSVM_pred,LR_score,LR_pred,Reliability_index,SiPhy_29way_logOdds,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,SIFT_score,SIFT_pred,CADD_raw,CADD_phred
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> As shown in the output below, apart from CADD.pm and Gwava.pm,
>>>>>>>>>>>> no scores are returned for the others. dbNSFP.pm should get at least CADD
>>>>>>>>>>>> scores because these exist. As recommended I tried using:
>>>>>>>>>>>>
>>>>>>>>>>>> sub feature_types {
>>>>>>>>>>>> return ['Feature', 'Intergenic'];
>>>>>>>>>>>> }
>>>>>>>>>>>>
>>>>>>>>>>>> or
>>>>>>>>>>>>
>>>>>>>>>>>> sub feature_types {
>>>>>>>>>>>> return ['Transcript', 'Intergenic'];
>>>>>>>>>>>> }
>>>>>>>>>>>>
>>>>>>>>>>>> in dbNFSP.pm but does not help. When I tried that in
>>>>>>>>>>>> TSSDistance.pm I get this error:
>>>>>>>>>>>>
>>>>>>>>>>>> Plugin 'TSSDistance' went wrong: Can't locate object method
>>>>>>>>>>>> "transcript" via package
>>>>>>>>>>>> "Bio::EnsEMBL::Variation::IntergenicVariationAllele" at
>>>>>>>>>>>> /media/sf_D_DRIVE/Projects/Databases/ensembl/Plugins//TSSDistance.pm line
>>>>>>>>>>>> 56.
>>>>>>>>>>>>
>>>>>>>>>>>> For UpDownDistance.pm, it does not seem to work as for instance rs140931361
>>>>>>>>>>>> is 58298 bp from ENSG00000198822 but this is gene is not
>>>>>>>>>>>> returned.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> OUTPUT:
>>>>>>>>>>>>
>>>>>>>>>>>> ## ENSEMBL VARIANT EFFECT PREDICTOR v75 ##
>>>>>>>>>>>> Output produced at 2014-05-07 17:28:44 ##
>>>>>>>>>>>> Connected to homo_sapiens_core_75_37 on ensembldb.ensembl.org ##
>>>>>>>>>>>> Using cache in /media/sf_D_DRIVE/Projects/Databases/ensembl//homo_sapiens/75 ##
>>>>>>>>>>>> Using API version 75, DB version 75 ##
>>>>>>>>>>>> sift version sift5.0.2 ##
>>>>>>>>>>>> polyphen version 2.2.2 ## Extra
>>>>>>>>>>>> column keys: ## BIOTYPE :
>>>>>>>>>>>> Biotype of transcript ##
>>>>>>>>>>>> CANONICAL : Indicates if transcript is canonical for this gene ##
>>>>>>>>>>>> CELL_TYPE : List of cell types and classifications for regulatory feature ##
>>>>>>>>>>>> CLIN_SIG : Clinical significance of variant from dbSNP ##
>>>>>>>>>>>> DISTANCE : Shortest distance from variant to transcript ##
>>>>>>>>>>>> DOMAINS : The source and identifer of any overlapping protein domains ##
>>>>>>>>>>>> ENSP : Ensembl protein identifer ##
>>>>>>>>>>>> EXON : Exon number(s) / total ##
>>>>>>>>>>>> HIGH_INF_POS : A flag indicating if the variant falls in a high information
>>>>>>>>>>>> position of the TFBP ## INTRON :
>>>>>>>>>>>> Intron number(s) / total ##
>>>>>>>>>>>> MOTIF_NAME : The source and identifier of a transcription factor binding
>>>>>>>>>>>> profile (TFBP) aligned at this position ##
>>>>>>>>>>>> MOTIF_POS : The relative position of the variation in the aligned TFBP ##
>>>>>>>>>>>> MOTIF_SCORE_CHANGE : The difference in motif score of the reference and
>>>>>>>>>>>> variant sequences for the TFBP ##
>>>>>>>>>>>> PUBMED : Pubmed ID(s) of publications that cite existing variant ##
>>>>>>>>>>>> PolyPhen : PolyPhen prediction and/or score ##
>>>>>>>>>>>> SIFT : SIFT prediction and/or score ##
>>>>>>>>>>>> SYMBOL : Gene symbol (e.g. HGNC) ##
>>>>>>>>>>>> SYMBOL_SOURCE : Source of gene symbol ##
>>>>>>>>>>>> TSSDistance : Distance from the transcription start site ##
>>>>>>>>>>>> Condel : Consensus deleteriousness score for an amino acid
>>>>>>>>>>>> substitution based on SIFT and PolyPhen-2 ##
>>>>>>>>>>>> CADD_RAW : Raw CADD score ##
>>>>>>>>>>>> CADD_PHRED : PHRED-like scaled CADD score ##
>>>>>>>>>>>> GWAVA : Genome Wide Annotation of VAriants score (tss model) ##
>>>>>>>>>>>> Conservation : The conservation score for this site
>>>>>>>>>>>> (method_link_type="GERP_CONSERVATION_SCORE", species_set="mammals") ##
>>>>>>>>>>>> MutationTaster_score : MutationTaster_score from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> Polyphen2_HVAR_score : Polyphen2_HVAR_score from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> LRT_pred : LRT_pred from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> MutationAssessor_score : MutationAssessor_score from dbNSFP
>>>>>>>>>>>> file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> FATHMM_pred : FATHMM_pred from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> LR_score : LR_score from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> MutationTaster_pred : MutationTaster_pred from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> SiPhy_29way_logOdds : SiPhy_29way_logOdds from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> CADD_phred : CADD_phred from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> Polyphen2_HVAR_pred : Polyphen2_HVAR_pred from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> RadialSVM_pred : RadialSVM_pred from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> Reliability_index : Reliability_index from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> GERP++_NR : GERP++_NR from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> MutationAssessor_pred : MutationAssessor_pred from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> LRT_score : LRT_score from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> CADD_raw : CADD_raw from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> LR_pred : LR_pred from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> FATHMM_score : FATHMM_score from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> SIFT_score : SIFT_score from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> GERP++_RS : GERP++_RS from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> SIFT_pred : SIFT_pred from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz ##
>>>>>>>>>>>> RadialSVM_score : RadialSVM_score from dbNSFP file
>>>>>>>>>>>> /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz
>>>>>>>>>>>> #Uploaded_variation Location Allele Existing_variation SYMBOL
>>>>>>>>>>>> SYMBOL_SOURCE Gene ENSP Feature Feature_type BIOTYPE STRAND
>>>>>>>>>>>> CANONICAL EXON INTRON DISTANCE TSSDistance Consequence
>>>>>>>>>>>> cDNA_position CDS_position Protein_position Amino_acids Codons
>>>>>>>>>>>> PolyPhen SIFT Condel CELL_TYPE SV PUBMED CLIN_SIG HIGH_INF_POS
>>>>>>>>>>>> MOTIF_NAME MOTIF_POS MOTIF_SCORE_CHANGE TSSDistance CADD_RAW
>>>>>>>>>>>> CADD_PHRED GWAVA Conservation GERP++_NR GERP++_RS LRT_score
>>>>>>>>>>>> LRT_pred MutationTaster_score MutationTaster_pred
>>>>>>>>>>>> MutationAssessor_score MutationAssessor_pred FATHMM_score
>>>>>>>>>>>> FATHMM_pred RadialSVM_score RadialSVM_pred LR_score LR_pred
>>>>>>>>>>>> Reliability_index SiPhy_29way_logOdds Polyphen2_HVAR_score
>>>>>>>>>>>> Polyphen2_HVAR_pred SIFT_score SIFT_pred CADD_raw CADD_phred
>>>>>>>>>>>> Extra rs13247133 7:86199080 A rs13247133 - - - - - - - - - - -
>>>>>>>>>>>> - - intergenic_variant - - - - - - - - - - - - - - - - -
>>>>>>>>>>>> -0.25769 2.762 0.11 - - - - - - - - - - - - - - - - - - - - - -
>>>>>>>>>>>> - CADD_RAW=-0.257691;CADD_PHRED=2.762;GWAVA=0.11 rs13244782
>>>>>>>>>>>> 7:86202665 T rs13244782 - - - - - - - - - - - - -
>>>>>>>>>>>> intergenic_variant - - - - - - - - - - - - - - - - - 1.957591
>>>>>>>>>>>> 12.5 0.15 - - - - - - - - - - - - - - - - - - - - - - -
>>>>>>>>>>>> CADD_RAW=1.957591;CADD_PHRED=12.50;GWAVA=0.15 rs12704267
>>>>>>>>>>>> 7:86206830 T rs12704267 - - - - - - - - - - - - -
>>>>>>>>>>>> intergenic_variant - - - - - - - - - - - - - - - - - 0.111018
>>>>>>>>>>>> 4.597 0.16 - - - - - - - - - - - - - - - - - - - - - - -
>>>>>>>>>>>> CADD_RAW=0.111018;CADD_PHRED=4.597;GWAVA=0.16 rs140931361
>>>>>>>>>>>> 7:86214933-86214937 - rs140931361 - - - - - - - - - - - - -
>>>>>>>>>>>> intergenic_variant - - - - - - - - - - - - - - - - - -0.42024
>>>>>>>>>>>> 2.04 - - - - - - - - - - - - - - - - - - - - - - - -
>>>>>>>>>>>> CADD_RAW=-0.420243;CADD_PHRED=2.040 rs34536358 7:86222651 G
>>>>>>>>>>>> rs34536358 - - - - - - - - - - - - - intergenic_variant - - - -
>>>>>>>>>>>> - - - - - - - - - - - - - -0.31002 2.524 0.18 - - - - - - - - -
>>>>>>>>>>>> - - - - - - - - - - - - - -
>>>>>>>>>>>> CADD_RAW=-0.310016;CADD_PHRED=2.524;GWAVA=0.18 rs36006360
>>>>>>>>>>>> 7:86224933 T rs36006360 - - - - - - - - - - - - -
>>>>>>>>>>>> intergenic_variant - - - - - - - - - - - - - - - - - 2.513017
>>>>>>>>>>>> 14.36 0.36 - - - - - - - - - - - - - - - - - - - - - - -
>>>>>>>>>>>> CADD_RAW=2.513017;CADD_PHRED=14.36;GWAVA=0.36 rs13244678
>>>>>>>>>>>> 7:86232583 T rs13244678 - - - - - - - - - - - - -
>>>>>>>>>>>> intergenic_variant - - - - - - - - - - - - - - - - - -0.52024
>>>>>>>>>>>> 1.626 0.05 - - - - - - - - - - - - - - - - - - - - - - -
>>>>>>>>>>>> CADD_RAW=-0.520238;CADD_PHRED=1.626;GWAVA=0.05 rs12704279
>>>>>>>>>>>> 7:86238294 T rs12704279 - - - - - - - - - - - - -
>>>>>>>>>>>> intergenic_variant - - - - - - - - - - - - - - - - - 0.454708
>>>>>>>>>>>> 6.469 0.16 - - - - - - - - - - - - - - - - - - - - - - -
>>>>>>>>>>>> CADD_RAW=0.454708;CADD_PHRED=6.469;GWAVA=0.16 rs13228078
>>>>>>>>>>>> 7:86240691 C rs13228078 - - - - - - - - - - - - -
>>>>>>>>>>>> intergenic_variant - - - - - - - - - - - - - - - - - 0.980262
>>>>>>>>>>>> 9.002 0.1 - - - - - - - - - - - - - - - - - - - - - - -
>>>>>>>>>>>> CADD_RAW=0.980262;CADD_PHRED=9.002;GWAVA=0.1 rs140931361
>>>>>>>>>>>> 7:86214933-86214937 - rs140931361 - - - - - - - - - - - - -
>>>>>>>>>>>> intergenic_variant - - - - - - - - - - - - - - - - - -0.42024
>>>>>>>>>>>> 2.04 - - - - - - - - - - - - - - - - - - - - - - - -
>>>>>>>>>>>> CADD_RAW=-0.420243;CADD_PHRED=2.040
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>
>>>>>>>>>>>> G.
>>>>>>>>>>>>
>>>>>>>>>>>> On 7 May 2014 16:13, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hello,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Correct, the plugin was intended to work with
>>>>>>>>>>>>> the whole_genome_SNVs.tsv file, which only contains data for SNVs.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I've modified the plugin so that it should be able to cope
>>>>>>>>>>>>> with indel data files such as you have; please do let me know if you have
>>>>>>>>>>>>> any problems as I've only sparingly tested it on made-up data!
>>>>>>>>>>>>>
>>>>>>>>>>>>> Regards
>>>>>>>>>>>>>
>>>>>>>>>>>>> Will McLaren
>>>>>>>>>>>>> Ensembl Variation
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On 7 May 2014 15:37, Genomeo Dev <genomeodev at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> There seem to be a discrepancy between the CADD score
>>>>>>>>>>>>>> calculated using VEP with the CADD.pm plugin and the tabix direct output:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> For example using this 1000G variant:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> #CHROM POS ID REF ALT QUAL FILTER INFO
>>>>>>>>>>>>>> 7 86214932 rs140931361 TTACTC T . PASS .
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> variant_effect_predictor.pl -i input.txt --format vcf
>>>>>>>>>>>>>> --plugin CADD,/media/sf_D_DRIVE/Projects/Databases/CADD/v1.0/1000G.tsv.gz
>>>>>>>>>>>>>> does not return any CADD score
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> whereas
>>>>>>>>>>>>>> $ tabix -p vcf 1000G.tsv.gz 7:86214932-86214932
>>>>>>>>>>>>>> 7 86214932 TTACTC T -0.420243 2.040
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> This seems to affect indels and not SNVs. I could see in the
>>>>>>>>>>>>>> plugin that there is a rule to ignore indels. Any suggestions please how to
>>>>>>>>>>>>>> safely change that?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Also, in the plugin, I assume there is a test to ensure the
>>>>>>>>>>>>>> alleles are identical between the input file and the 1000G.tsv.gz file. Is
>>>>>>>>>>>>>> this correct?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> G.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>>>>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>>>>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>>>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>>>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> G.
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> G.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> G.
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> G.
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> G.
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> G.
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> G.
>>>>
>>>
>>>
>>>
>>> --
>>> G.
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
>
> --
> G.
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
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