update Ensembl VEP naming for VEP plugins

AVADA.pm

@@ -35,7 +35,7 @@ Automatic VAriant evidence DAtabase is a novel machine learning tool that uses n
 to automatically identify pathogenic genetic variant evidence in full-text primary literature about 
 monogenic disease and convert it to genomic coordinates.
 
-Please cite the AVADA publication alongside the VEP if you use this resource:
+Please cite the AVADA publication alongside Ensembl VEP if you use this resource:
 https://pubmed.ncbi.nlm.nih.gov/31467448/
 
 NB: The plugin currently does not annotate for downstream_gene_variant and upstream_gene_variant.

AlphaMissense.pm

@@ -70,7 +70,7 @@ limitations under the License.
  https://creativecommons.org/licenses/by/4.0/legalcode.
  Use of the AlphaMissense Database is subject to Google Cloud Platform Terms of Service  
 
- Please cite the AlphaMissense publication alongside the VEP
+ Please cite the AlphaMissense publication alongside Ensembl VEP
  if you use this resource: https://doi.org/10.1126/science.adg7492
 
  Disclaimer: The AlphaMissense Database and other information provided on or linked to this site is 

AncestralAllele.pm

@@ -32,15 +32,15 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that retrieves ancestral allele sequences from a FASTA file.
+ An Ensembl VEP plugin that retrieves ancestral allele sequences from a FASTA file.
 
  Ensembl produces FASTA file dumps of the ancestral sequences of key species.
  - Data files for GRCh37: https://ftp.ensembl.org/pub/release-75/fasta/ancestral_alleles/
  - Data files for GRCh38: https://ftp.ensembl.org/pub/current_fasta/ancestral_alleles/
 
  For optimal retrieval speed, you should pre-process the FASTA files into a single
- bgzipped file that can be accessed via 'Bio::DB::HTS::Faidx' (installed by VEP's
- INSTALL.pl):
+ bgzipped file that can be accessed via 'Bio::DB::HTS::Faidx' (installed by
+ INSTALL.pl - see Ensembl/ensembl-vep repository):
 
  wget https://ftp.ensembl.org/pub/current_fasta/ancestral_alleles/homo_sapiens_ancestor_GRCh38.tar.gz
  tar xfz homo_sapiens_ancestor_GRCh38.tar.gz
@@ -96,7 +96,7 @@ sub new {
   die("ERROR: Bio::DB::HTS required to access compressed FASTA file $fasta_file\n") if $type eq 'Bio::DB::HTS::Faidx' && !$CAN_USE_FAIDX;
   $self->index_type($type);
 
-  # init DB here so indexing doesn't happen at some point in the middle of VEP run
+  # init DB here so indexing doesn't happen at some point in the middle of a run
   $self->fasta_db;
 
   return $self;

BayesDel.pm

@@ -33,15 +33,15 @@ limitations under the License.
 =head1 DESCRIPTION
 
  This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
- adds the BayesDel scores to VEP output.
+ adds the BayesDel scores to Ensembl VEP output.
 
  BayesDel is a deleteriousness meta-score combining multiple deleteriousness predictors to create an overall score. It works for coding and non-coding variants,
  single nucleotide variants and small insertion/deletions.
  The range of the score is from -1.29334 to 0.75731.
  The higher the score, the more likely the variant is pathogenic.
  For more information please visit: https://fenglab.chpc.utah.edu/BayesDel/BayesDel.html
 
- Please cite the BayesDel publication alongside the Ensembl VEP if you use this resource:
+ Please cite the BayesDel publication alongside Ensembl VEP if you use this resource:
  https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23158
 
 

Blosum62.pm

@@ -35,7 +35,7 @@ limitations under the License.
  This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
  looks up the BLOSUM 62 substitution matrix score for the reference
  and alternative amino acids predicted for a missense mutation. It adds
- one new entry to the VEP's Extra column, BLOSUM62 which is the 
+ one new entry to the output, BLOSUM62, which is the 
  associated score. 
 
 =cut

CADD.pm

@@ -34,10 +34,10 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that retrieves CADD scores for variants from one or more
+ An Ensembl VEP plugin that retrieves CADD scores for variants from one or more
  tabix-indexed CADD data files.
 
- Please cite the CADD publication alongside the VEP if you use this resource:
+ Please cite the CADD publication alongside Ensembl VEP if you use this resource:
  https://www.ncbi.nlm.nih.gov/pubmed/24487276
 
  The tabix utility must be installed in your path to use this plugin. 

CAPICE.pm

@@ -38,10 +38,10 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that retrieves CAPICE scores for variants from one or more
+ An Ensembl VEP plugin that retrieves CAPICE scores for variants from one or more
  tabix-indexed CAPICE data files, in order to predict their pathogenicity.
 
- Please cite the CAPICE publication alongside the VEP if you use this resource:
+ Please cite the CAPICE publication alongside Ensembl VEP if you use this resource:
  https://pubmed.ncbi.nlm.nih.gov/32831124/
 
  The tabix utility must be installed in your path to use this plugin. The CAPICE

CCDSFilter.pm

@@ -32,7 +32,7 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A simple VEP filter plugin that limits output to variants that
+ A simple example Ensembl VEP filter plugin that limits output to variants that
  fall in transcripts which have CCDS coding sequences.
 
 =cut

Carol.pm

@@ -32,11 +32,11 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that calculates the Combined Annotation scoRing toOL (CAROL)
+ An Ensembl VEP plugin that calculates the Combined Annotation scoRing toOL (CAROL)
  score (1) for a missense mutation based on the pre-calculated SIFT (2) and
  PolyPhen-2 (3) scores from the Ensembl API (4).
 
- It adds one new entry class to the VEP's Extra column, CAROL which is
+ It adds one new entry to the output, CAROL, which is
  the calculated CAROL score. Note that this module is a perl reimplementation of 
  the original R script, available at: https://sanger.ac.uk/tool/carol/
 

ClinPred.pm

@@ -27,7 +27,7 @@ limitations under the License.
  This is a plugin for the Ensembl Variant Effect Predictor (VEP) that adds pre-calculated scores from ClinPred.
  ClinPred is a prediction tool to identify disease-relevant nonsynonymous variants.
 
- Please cite the ClinPred publication alongside the VEP if you use this resource:
+ Please cite the ClinPred publication alongside Ensembl VEP if you use this resource:
  https://www.sciencedirect.com/science/article/pii/S0002929718302714
 
  ClinPred scores can be downloaded from 

Condel.pm

@@ -32,11 +32,11 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that calculates the Consensus Deleteriousness (Condel) score (1)
+ An Ensembl VEP plugin that calculates the Consensus Deleteriousness (Condel) score (1)
  for a missense mutation based on the pre-calculated SIFT (2) and PolyPhen-2 (3)
  scores from the Ensembl API (4).
 
- It adds one new entry class to the VEP's Extra column, Condel which is the
+ It adds one new entry to the output, Condel, which is the
  calculated Condel score. This version of Condel was developed by the Biomedical
  Genomics Group  of the Universitat Pompeu Fabra, at the Barcelona Biomedical
  Research Park and available at https://bg.upf.edu/condel. The code in this

DAS.pm

@@ -25,7 +25,7 @@
 
 =head1 DESCRIPTION
 
- A simple VEP plugin that checks for DAS features overlapping variants. Currently assumes that
+ An Ensembl VEP plugin that checks for DAS features overlapping variants. Currently assumes that
  the assemblies match, and doesn't do any smart fetching of chunks of features (i.e. the plugin
  will query the DAS server once for every variant in the input file).
 

DeNovo.pm

@@ -33,7 +33,7 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that identifies de novo variants in a VCF file.
+ An Ensembl VEP plugin that identifies de novo variants in a VCF file.
  The plugin is not compatible with JSON output format.
 
  Options are passed to the plugin as key=value pairs:

DosageSensitivity.pm

@@ -33,11 +33,11 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that retrieves haploinsufficiency and triplosensitivity probability scores
+ An Ensembl VEP plugin that retrieves haploinsufficiency and triplosensitivity probability scores
  for affected genes from a dosage sensitivity catalogue published in paper -
  https://www.sciencedirect.com/science/article/pii/S0092867422007887
 
- Please cite the above publication alongside the VEP if you use this resource.
+ Please cite the above publication alongside Ensembl VEP if you use this resource.
 
  This plugin returns two scores:
  - pHaplo score gives the probability of a gene being haploinsufficient (deletion intolerant)

Downstream.pm

@@ -43,7 +43,7 @@ limitations under the License.
  translation. Any variants with a splice site consequence type are
  ignored.
 
- If VEP is run in offline mode using the flag --offline, a FASTA file is required.
+ In run in offline mode, using the flag --offline, a FASTA file is required.
  See: https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#fasta
  Sequence may be incomplete without a FASTA file or database connection.
 

Draw.pm

@@ -32,7 +32,7 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that draws pictures of the transcript model showing the
+ An Ensembl VEP plugin that draws pictures of the transcript model showing the
  variant location.
 
  Takes five optional paramters:

EVE.pm

@@ -40,7 +40,7 @@ limitations under the License.
  and does not merge input lines to report on adjacent variants.
  It is only available for GRCh38.
 
- Please cite EVE publication alongside the VEP if you use this resource:
+ Please cite EVE publication alongside Ensembl VEP if you use this resource:
  https://www.nature.com/articles/s41586-021-04043-8
 
 ###################################################

Enformer.pm

@@ -30,7 +30,7 @@ limitations under the License.
 
  This plugin is available for GRCh37 and GRCh38
 
- Please cite the Enformer publication alongside the VEP if you use this resource:
+ Please cite the Enformer publication alongside Ensembl VEP if you use this resource:
  https://www.nature.com/articles/s41592-021-01252-x
 
  GRCh38 scores were lifted over using CrossMap from the Enformer scores available here - https://console.cloud.google.com/storage/browser/dm-enformer/variant-scores/1000-genomes/enformer

FATHMM.pm

@@ -32,7 +32,7 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that gets FATHMM scores and predictions for missense variants.
+ An Ensembl VEP plugin that gets FATHMM scores and predictions for missense variants.
 
  You will need the fathmm.py script and its dependencies (Python, Python
  MySQLdb). You should create a "config.ini" file in the same directory as the

FATHMM_MKL.pm

@@ -32,7 +32,7 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that retrieves FATHMM-MKL scores for variants from a tabix-indexed
+ An Ensembl VEP plugin that retrieves FATHMM-MKL scores for variants from a tabix-indexed
  FATHMM-MKL data file.
 
  See https://github.com/HAShihab/fathmm-MKL for details.

FlagLRG.pm

@@ -31,7 +31,7 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that retrieves the LRG ID matching either the RefSeq or Ensembl
+ An Ensembl VEP plugin that retrieves the LRG ID matching either the RefSeq or Ensembl
  transcript IDs.
 
  You can obtain the 'list_LRGs_transcripts_xrefs.txt' using:

FunMotifs.pm

@@ -34,15 +34,15 @@ limitations under the License.
  Parameters Required:
 
  [0] : FunMotifs BED file
- [1]+ : List of columns to include within VEP output (e.g. fscore, skin, contactingdomain)
+ [1]+ : List of columns to include within the output (e.g. fscore, skin, contactingdomain)
 
 
 =head1 DESCRIPTION
 
  This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
- adds tissue-specific transcription factor motifs from FunMotifs to VEP output.
+ adds tissue-specific transcription factor motifs from FunMotifs to the output.
 
- Please cite the FunMotifs publication alongside the VEP if you use this resource. 
+ Please cite the FunMotifs publication alongside Ensembl VEP if you use this resource. 
  The preprint can be found at: https://www.biorxiv.org/content/10.1101/683722v1
 
  FunMotifs files can be downloaded from: http://bioinf.icm.uu.se:3838/funmotifs/

G2P.pm

@@ -31,7 +31,7 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that uses G2P allelic requirements to assess variants in genes
+ An Ensembl VEP plugin that uses G2P allelic requirements to assess variants in genes
  for potential phenotype involvement.
 
  The plugin has multiple configuration options, though minimally requires only
@@ -450,7 +450,7 @@ sub new {
   $self->{config}->{sift} = 'b';
   $self->{config}->{polyphen} = 'b';
 
-  # tell VEP we have a cache so stuff gets shared/merged between forks
+  # we have a cache; needs those data to get shared/merged between forks
   $self->{has_cache} = 1;
   $self->{cache}->{g2p_in_vcf} = {};
 
@@ -503,7 +503,7 @@ sub get_header_info {
                 - variant include list
                 - allele frequency
                Based on the filtering results check if the allelic requirement is fulfilled and write results to hash.
-               Dump annnotations to a log file for generating TXT and HTML output files after VEP has finished.
+               Dump annnotations to a log file for generating TXT and HTML output files after run has finished.
   Returntype : Hashref $results
   Exceptions : None
   Caller     : General

GO.pm

@@ -47,14 +47,14 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that retrieves Gene Ontology (GO) terms associated with
+ An Ensembl VEP plugin that retrieves Gene Ontology (GO) terms associated with
  transcripts (e.g. GRCh38) or their translations (e.g. GRCh37) using custom
  GFF annotation containing GO terms.
 
  The custom GFF files are automatically created if the input file do not exist
  by querying the Ensembl core database, according to database version, species
- and assembly used in VEP. Note that automatic retrieval fails if using the
- --offline option.
+ and assembly used in Ensembl VEP. Note that automatic retrieval fails if using 
+ the --offline option.
 
  The GFF files containing the GO terms are saved to and loaded from the working
  directory by default. To change this, provide a directory path as an argument:

GWAS.pm

@@ -33,13 +33,13 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that retrieves relevant NHGRI-EBI GWAS Catalog data given the file. 
+ An Ensembl VEP plugin that retrieves relevant NHGRI-EBI GWAS Catalog data given the file. 
 
  This plugin supports both the curated data that is found in the download section of the NHGRI-EBI GWAS Catalog website and the 
  summary statistics file. By default the plugin assumes the file provided is the curated file but you can pass "type=sstate" 
  to say you want to annotate with a summary statistics file.
 
- Please cite the following publication alongside the VEP if you use this resource:
+ Please cite the following publication alongside Ensembl VEP if you use this resource:
  https://pubmed.ncbi.nlm.nih.gov/30445434/
 
  Pre-requisites:

GeneBe.pm

@@ -31,10 +31,10 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A user-contributed VEP plugin that retrieves automatic ACMG variant classification data from
+ A user-contributed Ensembl VEP plugin that retrieves automatic ACMG variant classification data from
  https://genebe.net/
 
- Please cite the GeneBe publication alongside the VEP if you use this resource:
+ Please cite the GeneBe publication alongside Ensembl VEP if you use this resource:
  https://onlinelibrary.wiley.com/doi/10.1111/cge.14516 .
 
  Please be advised that the GeneBe API is freely accessible for academic purposes only, with a limited

GeneSplicer.pm

@@ -94,7 +94,7 @@ limitations under the License.
  Example:
    --plugin GeneSplicer,binary=$GS/bin/linux/genesplicer,training=$GS/human,context=200,tmpdir=/mytmp
 
- When using VEP Docker/Singularity, the `binary` argument can be ommitted, as
+ When using Ensembl VEP Docker/Singularity, the `binary` argument can be ommitted, as
  the `genesplicer` command is exported in the $PATH variable and is thus
  automatically detected by the plugin:
    --plugin GeneSplicer,training=$GS/human,context=200,tmpdir=/mytmp

Geno2MP.pm

@@ -38,7 +38,7 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that adds information from Geno2MP, a web-accessible database of
+ An Ensembl VEP plugin that adds information from Geno2MP, a web-accessible database of
  rare variant genotypes linked to phenotypic information.
 
  Parameters can be set using a key=value system:
@@ -48,7 +48,7 @@ limitations under the License.
    url  : build and return URL to Geno2MP variant page (boolean; 0 by default);
           the variant location in Geno2MP website is based on GRCh37 coordinates
 
- Please cite Geno2MP alongside the VEP if you use this resource:
+ Please cite Geno2MP alongside Ensembl VEP if you use this resource:
  Geno2MP, NHGRI/NHLBI University of Washington-Center for Mendelian Genomics (UW-CMG), Seattle, WA
  (URL: http://geno2mp.gs.washington.edu [date (month, yr) accessed]).
 

HGVSIntronOffset.pm

@@ -31,7 +31,7 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin for the Ensembl Variant Effect Predictor (VEP) that returns
+ An Ensembl VEP plugin for the Ensembl Variant Effect Predictor (VEP) that returns
  HGVS intron start and end offsets. To be used with --hgvs option.
 
 =cut

IntAct.pm

@@ -33,9 +33,9 @@ limitations under the License.
 
 =head1 DESCRIPTION
 
- A VEP plugin that retrieves molecular interaction data for variants as reprted by IntAct database.
+ An Ensembl VEP plugin that retrieves molecular interaction data for variants as reprted by IntAct database.
 
- Please cite the IntAct publication alongside the VEP if you use this resource:
+ Please cite the IntAct publication alongside Ensembl VEP if you use this resource:
  https://pubmed.ncbi.nlm.nih.gov/24234451/
 
  Pre-requisites:
@@ -75,7 +75,7 @@ limitations under the License.
  See what these options mean - https://www.ebi.ac.uk/intact/download/datasets#mutations
 
  Note that, interaction accession can be used to link to full details on the interaction website. For example, 
- where the VEP output reports an interaction_ac of EBI-12501485, the URL would be : 
+ where the output reports an interaction_ac of EBI-12501485, the URL would be : 
 
    https://www.ebi.ac.uk/intact/details/interaction/EBI-12501485