[ensembl-dev] UpDownDistance using
Genomeo Dev
genomeodev at gmail.com
Fri May 30 15:48:18 BST 2014
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.
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