[ensembl-dev] UpDownDistance using
Genomeo Dev
genomeodev at gmail.com
Mon Jun 2 09:34:52 BST 2014
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:
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>>>>>>>>>>> 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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>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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/
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>>>> Posting guidelines and subscribe/unsubscribe info:
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>>>>
>>>
>>>
>>> --
>>> G.
>>>
>>
>>
>>
>> --
>> G.
>>
>
>
>
> --
> G.
>
--
G.
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