[ensembl-dev] UpDownDistance using

Genomeo Dev genomeodev at gmail.com
Fri May 30 13:01:34 BST 2014


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:
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>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
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-- 
G.
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