Change script name to vep

Ensembl · Feb 28, 2017 · 9230f25 · 9230f25
1 parent ac319a5
commit 9230f25
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diff --git a/Blosum62.pm b/Blosum62.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv Blosum62.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin Blosum62
+ ./vep -i variations.vcf --plugin Blosum62
 
 =head1 DESCRIPTION
 

diff --git a/CADD.pm b/CADD.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv CADD.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin CADD,whole_genome_SNVs.tsv.gz,InDels.tsv.gz
+ ./vep -i variations.vcf --plugin CADD,whole_genome_SNVs.tsv.gz,InDels.tsv.gz
 
 =head1 DESCRIPTION
 

diff --git a/CCDSFilter.pm b/CCDSFilter.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv CCDSFilter.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin CCDSFilter
+ ./vep -i variations.vcf --plugin CCDSFilter
 
 =head1 DESCRIPTION
 

diff --git a/CSN.pm b/CSN.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
   mv CSN.pm ~/.vep/Plugins
-  perl variant_effect_predictor.pl -i variations.vcf --cache --plugin CSN
+  ./vep -i variations.vcf --cache --plugin CSN
 
 =head1 DESCRIPTION
 

diff --git a/Carol.pm b/Carol.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv Carol.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin Carol
+ ./vep -i variations.vcf --plugin Carol
 
 =head1 DESCRIPTION
 

diff --git a/Condel.pm b/Condel.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv Condel.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin Condel,/path/to/config/Condel/config,b
+ ./vep -i variations.vcf --plugin Condel,/path/to/config/Condel/config,b
 
 =head1 DESCRIPTION
 

diff --git a/Conservation.pm b/Conservation.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv Conservation.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin Conservation,GERP_CONSERVATION_SCORE,mammals
+ ./vep -i variations.vcf --plugin Conservation,GERP_CONSERVATION_SCORE,mammals
 
 =head1 DESCRIPTION
 

diff --git a/DAS.pm b/DAS.pm
@@ -21,7 +21,7 @@
 =head1 SYNOPSIS
 
  mv DAS.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin DAS,<DAS_server>,<DAS_source>,<proxy>
+ ./vep -i variations.vcf --plugin DAS,<DAS_server>,<DAS_source>,<proxy>
 
 =head1 DESCRIPTION
 
@@ -35,7 +35,7 @@
  multiple times, e.g.:
 
  export DAS="http://somewhere/das"
- perl variant_effect_predictor.pl -i variations.vcf --plugin DAS,$DAS,source1 --plugin DAS,$DAS,source2
+ ./vep -i variations.vcf --plugin DAS,$DAS,source1 --plugin DAS,$DAS,source2
 
  Requires the Bio::Das::Lite module from CPAN.
 

diff --git a/Downstream.pm b/Downstream.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv Downstream.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin Downstream
+ ./vep -i variations.vcf --plugin Downstream
 
 =head1 DESCRIPTION
 

diff --git a/Draw.pm b/Draw.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv Draw.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin Draw
+ ./vep -i variations.vcf --plugin Draw
 
 =head1 DESCRIPTION
 
@@ -43,7 +43,7 @@ limitations under the License.
  
  e.g.
  
- perl variant_effect_predictor.pl -i variations.vcf --plugin Draw,myimg,2000,100
+ ./vep -i variations.vcf --plugin Draw,myimg,2000,100
  
  Images are written to [file_stem]_[transcript_id]_[variant_id].png
  

diff --git a/ExAC.pm b/ExAC.pm
@@ -28,10 +28,10 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv ExAC.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin ExAC,/path/to/ExAC/ExAC.r0.3.sites.vep.vcf.gz
- perl variant_effect_predictor.pl -i variations.vcf --plugin ExAC,/path/to/ExAC/ExAC.r0.3.sites.vep.vcf.gz,AC
- perl variant_effect_predictor.pl -i variations.vcf --plugin ExAC,/path/to/ExAC/ExAC.r0.3.sites.vep.vcf.gz,,AN
- perl variant_effect_predictor.pl -i variations.vcf --plugin ExAC,/path/to/ExAC/ExAC.r0.3.sites.vep.vcf.gz,AC,AN
+ ./vep -i variations.vcf --plugin ExAC,/path/to/ExAC/ExAC.r0.3.sites.vep.vcf.gz
+ ./vep -i variations.vcf --plugin ExAC,/path/to/ExAC/ExAC.r0.3.sites.vep.vcf.gz,AC
+ ./vep -i variations.vcf --plugin ExAC,/path/to/ExAC/ExAC.r0.3.sites.vep.vcf.gz,,AN
+ ./vep -i variations.vcf --plugin ExAC,/path/to/ExAC/ExAC.r0.3.sites.vep.vcf.gz,AC,AN
 
 
 

diff --git a/ExACpLI.pm b/ExACpLI.pm
@@ -33,7 +33,7 @@ ExACpLI - Add ExAC pLI to the VEP output
 
   mv ExACpLI.pm ~/.vep/Plugins
   mv ExACpLI_values.txt ~/.vep/Plugins
-  perl vep.pl -i variants.vcf --plugin ExACpLI
+  ./vep -i variants.vcf --plugin ExACpLI
 
 =head1 DESCRIPTION
 
@@ -62,7 +62,7 @@ ExACpLI - Add ExAC pLI to the VEP output
 
   To use another values file, add it as a parameter i.e.
 
-     perl vep.pl -i variants.vcf --plugin ExACpLI,values_file.txt
+     ./vep -i variants.vcf --plugin ExACpLI,values_file.txt
 
 
 =cut

diff --git a/FATHMM.pm b/FATHMM.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv FATHMM.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin FATHMM,"python /path/to/fathmm/fathmm.py"
+ ./vep -i variations.vcf --plugin FATHMM,"python /path/to/fathmm/fathmm.py"
 
 =head1 DESCRIPTION
 

diff --git a/FATHMM_MKL.pm b/FATHMM_MKL.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv FATHMM_MKL.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i input.vcf --plugin FATHMM_MKL,fathmm-MKL_Current.tab.gz
+ ./vep -i input.vcf --plugin FATHMM_MKL,fathmm-MKL_Current.tab.gz
 
 =head1 DESCRIPTION
 

diff --git a/G2P.pm b/G2P.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv G2P.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin G2P,/path/to/G2P.csv.gz
+ ./vep -i variations.vcf --plugin G2P,/path/to/G2P.csv.gz
 
 =head1 DESCRIPTION
 

diff --git a/GO.pm b/GO.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv GO.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin GO
+ ./vep -i variations.vcf --plugin GO
 
 =head1 DESCRIPTION
 

diff --git a/GXA.pm b/GXA.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
   mv GXA.pm ~/.vep/Plugins
-  perl variant_effect_predictor.pl -i variations.vcf --cache --plugin GXA
+  ./vep -i variations.vcf --cache --plugin GXA
 
 =head1 DESCRIPTION
 

diff --git a/GeneSplicer.pm b/GeneSplicer.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv GeneSplicer.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variants.vcf --plugin GeneSplicer,[path_to_genesplicer_bin],[path_to_training_dir],[option1=value],[option2=value]
+ ./vep -i variants.vcf --plugin GeneSplicer,[path_to_genesplicer_bin],[path_to_training_dir],[option1=value],[option2=value]
 
 =head1 DESCRIPTION
 

diff --git a/HGVSshift.pm b/HGVSshift.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
   mv HGVSshift.pm ~/.vep/Plugins
-  perl variant_effect_predictor.pl -i variations.vcf --cache --plugin HGVSshift
+  ./vep -i variations.vcf --cache --plugin HGVSshift
 
 =head1 DESCRIPTION
 

diff --git a/LD.pm b/LD.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv LD.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin LD,1000GENOMES:pilot_1_CEU_low_coverage_panel,0.8
+ ./vep -i variations.vcf --plugin LD,1000GENOMES:pilot_1_CEU_low_coverage_panel,0.8
 
 =head1 DESCRIPTION
 
@@ -53,7 +53,7 @@ limitations under the License.
  'interesting' variants first. You can do this by supplying a filter
  plugin as an argument to the VEP before this one, e.g.:
 
-  perl variant_effect_predictor.pl -i variations.vcf --plugin MyFilter --plugin LD
+  ./vep -i variations.vcf --plugin MyFilter --plugin LD
 
 =cut
 

diff --git a/LOVD.pm b/LOVD.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv LOVD.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin LOVD
+ ./vep -i variations.vcf --plugin LOVD
 
 =head1 DESCRIPTION
 

diff --git a/LoFtool.pm b/LoFtool.pm
@@ -29,7 +29,7 @@ limitations under the License.
 
   mv LoFtool.pm ~/.vep/Plugins
   mv LoFtool_scores.txt ~/.vep/Plugins
-  perl variant_effect_predictor.pl -i variants.vcf --plugin LoFtool
+  ./vep -i variants.vcf --plugin LoFtool
 
 =head1 DESCRIPTION
 
@@ -51,7 +51,7 @@ limitations under the License.
 
   To use another scores file, add it as a parameter i.e.
 
-  perl variant_effect_predictor.pl -i variants.vcf --plugin LoFtool,scores_file.txt
+  ./vep -i variants.vcf --plugin LoFtool,scores_file.txt
 
 =cut
 

diff --git a/MaxEntScan.pm b/MaxEntScan.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv MaxEntScan.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variants.vcf --plugin MaxEntScan,[path_to_maxentscan_dir]
+ ./vep -i variants.vcf --plugin MaxEntScan,[path_to_maxentscan_dir]
 
 =head1 DESCRIPTION
 

diff --git a/NearestGene.pm b/NearestGene.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv NearestGene.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --cache --plugin NearestGene
+ ./vep -i variations.vcf --cache --plugin NearestGene
 
 =head1 DESCRIPTION
 

diff --git a/NonSynonymousFilter.pm b/NonSynonymousFilter.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv NonSynonymousFilter.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin NonSynonymousFilter
+ ./vep -i variations.vcf --plugin NonSynonymousFilter
 
 =head1 DESCRIPTION
 

diff --git a/PON_P2.pm b/PON_P2.pm
@@ -3,7 +3,7 @@
  
 =head1 SYNOPSIS
  mv PON_P2.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin PON_P2,/path/to/python/script/ponp2.py,hg37
+ ./vep -i variations.vcf --plugin PON_P2,/path/to/python/script/ponp2.py,hg37
  
 =head1 DESCRIPTION
  This plugin for Ensembl Variant Effect Predictor (VEP) computes the predictions of PON-P2

diff --git a/Phenotypes.pm b/Phenotypes.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv Phenotypes.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin Phenotypes
+ ./vep -i variations.vcf --plugin Phenotypes
 
 =head1 DESCRIPTION
 

diff --git a/PolyPhen_SIFT.pm b/PolyPhen_SIFT.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv PolyPhen_SIFT.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf -cache --plugin PolyPhen_SIFT
+ ./vep -i variations.vcf -cache --plugin PolyPhen_SIFT
 
 =head1 DESCRIPTION
 

diff --git a/ProteinSeqs.pm b/ProteinSeqs.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv ProteinSeqs.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin ProteinSeqs,reference.fa,mutated.fa
+ ./vep -i variations.vcf --plugin ProteinSeqs,reference.fa,mutated.fa
 
 =head1 DESCRIPTION
 

diff --git a/RankFilter.pm b/RankFilter.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv RankFilter.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin RankFilter,splice_region_variant
+ ./vep -i variations.vcf --plugin RankFilter,splice_region_variant
 
 =head1 DESCRIPTION
 

diff --git a/SameCodon.pm b/SameCodon.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv SameCodon.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin SameCodon
+ ./vep -i variations.vcf --plugin SameCodon
 
 =head1 DESCRIPTION
 

diff --git a/TSSDistance.pm b/TSSDistance.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv TSSDistance.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin CCDSFilter
+ ./vep -i variations.vcf --plugin CCDSFilter
 
 =head1 DESCRIPTION
 

diff --git a/UpDownDistance.pm b/UpDownDistance.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv UpDownDistance.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin UpDownDistance,10000
+ ./vep -i variations.vcf --plugin UpDownDistance,10000
 
 =head1 DESCRIPTION
 

diff --git a/VEPbrowse.pm b/VEPbrowse.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv VEPbrowse.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin VEPbrowse --individual JohnDoe
+ ./vep -i variations.vcf --plugin VEPbrowse --individual JohnDoe
 
 =head1 DESCRIPTION
 

diff --git a/dbNSFP.pm b/dbNSFP.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv dbNSFP.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin dbNSFP,/path/to/dbNSFP.gz,col1,col2
+ ./vep -i variations.vcf --plugin dbNSFP,/path/to/dbNSFP.gz,col1,col2
 
 =head1 DESCRIPTION
 

diff --git a/dbscSNV.pm b/dbscSNV.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
   mv dbscSNV.pm ~/.vep/Plugins
-  perl variant_effect_predictor.pl -i variations.vcf --plugin dbscSNV,/path/to/dbscSNV.txt.gz
+  ./vep -i variations.vcf --plugin dbscSNV,/path/to/dbscSNV.txt.gz
 
 =head1 DESCRIPTION
 

diff --git a/miRNA.pm b/miRNA.pm
@@ -28,7 +28,7 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv miRNA.pm ~/.vep/Plugins
- perl variant_effect_predictor.pl -i variations.vcf --plugin miRNA
+ ./vep -i variations.vcf --plugin miRNA
 
 =head1 DESCRIPTION