Update plugin docs

AlphaMissense.pm

@@ -46,15 +46,15 @@ limitations under the License.
 
  This plugin will add two annotations per missense variant:
 
- 'am_pathogenicity', a continuous score between 0 and 1 which can be interpreted as the predicted 
+ - 'am_pathogenicity', a continuous score between 0 and 1 which can be interpreted as the predicted 
  probability of the variant being pathogenic. 
 
- 'am_class' is the classification of the variant into one of three discrete categories:  
- 'Likely pathogenic', 'Likely benign', or 'ambiguous'. These are derived using the following 
-  thresholds of am_pathogenicity: 
-    'Likely benign' if am_pathogenicity < 0.34; 
-    'Likely pathogenic' if am_pathogenicity > 0.564; 
-    'ambiguous' otherwise. 
+ - 'am_class' is the classification of the variant into one of three discrete categories:  
+   'likely_pathogenic', 'likely_benign', or 'ambiguous'. These are derived using the following 
+   thresholds of am_pathogenicity: 
+     'likely_benign'     if 'am_pathogenicity' < 0.34; 
+     'likely_pathogenic' if 'am_pathogenicity' > 0.564; 
+     'ambiguous' otherwise. 
 
  These thresholds were chosen to achieve 90% precision for both pathogenic and benign ClinVar variants. 
  Note that AlphaMissense was not trained on ClinVar variants. Variants labeled as 'ambiguous' should be 
@@ -92,7 +92,7 @@ limitations under the License.
    file             : (mandatory) Tabix-indexed AlphaMissense data
    cols             : (optional) Colon-separated columns to print from
                       AlphaMissense data; if set to 'all', all columns are printed
-                      (default: Missense_pathogenicity:Missense_class)
+                      (default: 'Missense_pathogenicity:Missense_class')
    transcript_match : Only print data if transcript identifiers match those from
                       AlphaMissense data (default: 0)
 

AncestralAllele.pm

@@ -35,11 +35,11 @@ limitations under the License.
  A 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 are available from https://ftp.ensembl.org/pub/release-75/fasta/ancestral_alleles/
- Data files for GRCh38 are available from https://ftp.ensembl.org/pub/current_fasta/ancestral_alleles/
+ - 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
+ bgzipped file that can be accessed via 'Bio::DB::HTS::Faidx' (installed by VEP's
  INSTALL.pl):
 
  wget https://ftp.ensembl.org/pub/current_fasta/ancestral_alleles/homo_sapiens_ancestor_GRCh38.tar.gz
@@ -48,16 +48,15 @@ limitations under the License.
  rm -rf homo_sapiens_ancestor_GRCh38/ homo_sapiens_ancestor_GRCh38.tar.gz
  ./vep -i variations.vcf --plugin AncestralAllele,homo_sapiens_ancestor_GRCh38.fa.gz
 
- Data file is only available for GRCh38. 
- The plugin is also compatible with Bio::DB::Fasta and an uncompressed FASTA file.
+ The plugin is also compatible with 'Bio::DB::Fasta' and an uncompressed FASTA file.
 
  Note the first time you run the plugin with a newly generated FASTA file it will
  spend some time indexing the file. DO NOT INTERRUPT THIS PROCESS, particularly
- if you do not have Bio::DB::HTS installed.
+ if you do not have 'Bio::DB::HTS' installed.
 
  Special cases:
-   "-" represents an insertion
-   "?" indicates the chromosome could not be looked up in the FASTA
+   - '-' represents an insertion
+   - '?' indicates the chromosome could not be looked up in the FASTA
 
 =cut
 

BayesDel.pm

@@ -51,15 +51,15 @@ limitations under the License.
 
 
  For GRCh37:
- tar zxvf BayesDel_170824_addAF.tgz
- rm *.gz.tbi
- gunzip *.gz
- for f in BayesDel_170824_addAF_chr*; do grep -v "^#" $f >> BayesDel_170824_addAF.txt; done
- cat BayesDel_170824_addAF.txt | sort -k1,1 -k2,2n > BayesDel_170824_addAF_sorted.txt
- grep "^#" BayesDel_170824_addAF_chr1 > BayesDel_170824_addAF_all_scores.txt
- cat BayesDel_170824_addAF_sorted.txt >> BayesDel_170824_addAF_all_scores.txt
- bgzip BayesDel_170824_addAF_all_scores.txt
- tabix -s 1 -b 2 -e 2 BayesDel_170824_addAF_all_scores.txt.gz
+ > tar zxvf BayesDel_170824_addAF.tgz
+ > rm *.gz.tbi
+ > gunzip *.gz
+ > for f in BayesDel_170824_addAF_chr*; do grep -v "^#" $f >> BayesDel_170824_addAF.txt; done
+ > cat BayesDel_170824_addAF.txt | sort -k1,1 -k2,2n > BayesDel_170824_addAF_sorted.txt
+ > grep "^#" BayesDel_170824_addAF_chr1 > BayesDel_170824_addAF_all_scores.txt
+ > cat BayesDel_170824_addAF_sorted.txt >> BayesDel_170824_addAF_all_scores.txt
+ > bgzip BayesDel_170824_addAF_all_scores.txt
+ > tabix -s 1 -b 2 -e 2 BayesDel_170824_addAF_all_scores.txt.gz
 
  For GRCh38:
  Remap GRCh37 file

Condel.pm

@@ -43,18 +43,19 @@ limitations under the License.
  plugin is based on a script provided by this group and slightly reformatted to
  fit into the Ensembl API.
 
- The plugin takes 3 command line arguments, the first is the path to a Condel 
- configuration directory which contains cutoffs and the distribution files etc., 
- the second is either "s", "p", or "b" to output the Condel score, prediction or 
- both (the default is both), and the third argument is either 1 or 2 to use the 
- original version of Condel (1), or the newer version (2) - 2 is the default and 
- is recommended to avoid false positive predictions from Condel in some 
- circumstances.
+ The plugin takes 3 command line arguments by this order:
+ 1. Path to a Condel configuration directory which contains cutoffs and the
+    distribution files, etc.
+ 2. Output: output the Condel score ('s'), prediction ('p') or both ('b');
+    both ('b') is the default.
+ 3. Version of Condel to use: either 1 (original version) or 2 (newer version);
+    '2' is the default and is recommended to avoid false positive predictions
+    from Condel in some circumstances.
 
  An example Condel configuration file and a set of distribution files can be
- found in the config/Condel directory in this repository. You should edit the 
- config/Condel/config/condel_SP.conf file and set the 'condel.dir' parameter to
- the full path to the location of the config/Condel directory on your system.
+ found in the 'config/Condel' directory in this repository. You should edit the 
+ 'config/Condel/config/condel_SP.conf' file and set the 'condel.dir' parameter to
+ the full path to the location of the 'config/Condel' directory on your system.
 
  References:
 
@@ -76,7 +77,7 @@ limitations under the License.
  (4) Flicek P, et al.
      Ensembl 2012
      Nucleic Acids Research (2011)
-     doi: 10.1093/nar/gkr991
+     doi:10.1093/nar/gkr991
 
 =cut
 

DisGeNET.pm

@@ -64,9 +64,9 @@ limitations under the License.
   - diseases/phenotype names (optional)
   - dbSNP variant Identifier (optional)
 
+ This plugin uses file 'all_variant_disease_pmid_associations.tsv.gz'.
+ File can be downloaded from: https://www.disgenet.org/downloads.
  The following steps are necessary before running this plugin (tested with DisGeNET export date 2020-05-26):
- This plugin uses file 'all_variant_disease_pmid_associations.tsv.gz'
- File can be downloaded from: https://www.disgenet.org/downloads
 
  gunzip all_variant_disease_pmid_associations.tsv.gz
  awk '($1 ~ /^snpId/ || $2 ~ /NA/) {next} {print $0}' all_variant_disease_pmid_associations.tsv > all_variant_disease_pmid_associations_clean.tsv

Draw.pm

@@ -33,7 +33,9 @@ limitations under the License.
 =head1 DESCRIPTION
 
  A VEP plugin that draws pictures of the transcript model showing the
- variant location. Can take five optional paramters:
+ variant location.
+
+ Takes five optional paramters:
  
  1) File name stem for images
  2) Image width in pixels (default: 1000px)
@@ -45,7 +47,7 @@ limitations under the License.
  
  ./vep -i variations.vcf --plugin Draw,myimg,2000,100
  
- Images are written to [file_stem]_[transcript_id]_[variant_id].png
+ Images are written to '[file_stem]_[transcript_id]_[variant_id].png'
  
  Requires GD library installed to run.
 

EVE.pm

@@ -35,6 +35,7 @@ limitations under the License.
 
  This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
  adds information from EVE (evolutionary model of variant effect).
+
  This plugin only report EVE scores for input variants
  and does not merge input lines to report on adjacent variants.
  It is only available for GRCh38.

FlagLRG.pm

@@ -32,8 +32,9 @@ limitations under the License.
 =head1 DESCRIPTION
 
  A 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:
+ transcript IDs.
 
+ You can obtain the 'list_LRGs_transcripts_xrefs.txt' using:
  > wget https://ftp.ebi.ac.uk/pub/databases/lrgex/list_LRGs_transcripts_xrefs.txt
 
 =cut

G2P.pm

@@ -39,7 +39,7 @@ limitations under the License.
 
  For further information see:
  Thormann A, Halachev M, McLaren W, et al. Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP.
- Nature Communications. 2019 May;10(1):2373. DOI: 10.1038/s41467-019-10016-3. PMID: 31147538; PMCID: PMC6542828.
+ Nature Communications. 2019 May;10(1):2373. doi:10.1038/s41467-019-10016-3. PMID: 31147538; PMCID: PMC6542828.
 
 
  Options are passed to the plugin as key=value pairs, (defaults in parentheses):
@@ -64,47 +64,47 @@ limitations under the License.
                          Setting the value to 1 will overwrite any confidence levels provided with the
                          confidence_levels option.
  af_from_vcf           : set value to 1 to include allele frequencies from VCF file. 
-                         Specifiy the list of reference populations to include with --af_from_vcf_keys    
+                         Specifiy the list of reference populations to include with '--af_from_vcf_keys'
  af_from_vcf_keys      : VCF collections used for annotating variant alleles with observed
                          allele frequencies. Allele frequencies are retrieved from VCF files. If
-                         af_from_vcf is set to 1 but no VCF collections are specified with --af_from_vcf_keys
+                         af_from_vcf is set to 1 but no VCF collections are specified with '--af_from_vcf_keys'
                          all available VCF collections are included. 
-                         Available VCF collections: topmed, uk10k, gnomADe, gnomADe_r2.1.1, gnomADg, gnomADg_v3.1.2.
+                         Available VCF collections: 'topmed', 'uk10k', 'gnomADe', 'gnomADe_r2.1.1', 'gnomADg', 'gnomADg_v3.1.2'.
                          Separate multiple values with '&'.
                          VCF collections contain the following populations: 
-                         topmed : TOPMed (available for GRCh37 and GRCh38).
-                         uk10k : ALSPAC, TWINSUK (available for GRCh37 and GRCh38).
-                         gnomADe & gnomADe_r2.1.1 - gnomADe:AFR, gnomADe:ALL, gnomADe:AMR, gnomADe:ASJ, gnomADe:EAS, gnomADe:FIN, gnomADe:NFE, gnomADe:OTH, gnomADe:SAS (for GRCh37 and GRCh38 respectively).
-                         gnomADg & gnomADg_v3.1.2 - gnomADg:AFR, gnomADg:ALL, gnomADg:AMR, gnomADg:ASJ, gnomADg:EAS, gnomADg:FIN, gnomADg:NFE, gnomADg:OTH (for GRCh37 and GRCh38 respectively).
-                         Need to use af_from_vcf paramter to use this option. 
+                         * 'topmed' - TOPMed (available for GRCh37 and GRCh38).
+                         * 'uk10k' - ALSPAC, TWINSUK (available for GRCh37 and GRCh38).
+                         * 'gnomADe' & 'gnomADe_r2.1.1' - gnomADe:AFR, gnomADe:ALL, gnomADe:AMR, gnomADe:ASJ, gnomADe:EAS, gnomADe:FIN, gnomADe:NFE, gnomADe:OTH, gnomADe:SAS (for GRCh37 and GRCh38 respectively).
+                         * 'gnomADg' & 'gnomADg_v3.1.2' - gnomADg:AFR, gnomADg:ALL, gnomADg:AMR, gnomADg:ASJ, gnomADg:EAS, gnomADg:FIN, gnomADg:NFE, gnomADg:OTH (for GRCh37 and GRCh38 respectively).
+                         Need to use 'af_from_vcf' parameter to use this option. 
  default_af            : default frequency of the input variant if no frequency data is
                          found (0). This determines whether such variants are included;
                          the value of 0 forces variants with no frequency data to be
                          included as this is considered equivalent to having a frequency
-                         of 0. Set to 1 (or any value higher than af) to exclude them.
+                         of 0. Set to 1 (or any value higher than 'af') to exclude them.
  types                 : SO consequence types to include. Separate multiple values with '&'
-                         (splice_donor_variant,splice_acceptor_variant,stop_gained,
-                         frameshift_variant,stop_lost,initiator_codon_variant,
-                         inframe_insertion,inframe_deletion,missense_variant,
-                         coding_sequence_variant,start_lost,transcript_ablation,
-                         transcript_amplification,protein_altering_variant)
+                         (splice_donor_variant, splice_acceptor_variant, stop_gained,
+                         frameshift_variant, stop_lost, initiator_codon_variant,
+                         inframe_insertion, inframe_deletion,missense_variant,
+                         coding_sequence_variant, start_lost,transcript_ablation,
+                         transcript_amplification, protein_altering_variant)
 
   log_dir              : write stats to log files in log_dir 
 
   txt_report           : write all G2P complete genes and attributes to txt file
 
   html_report          : write all G2P complete genes and attributes to html file
 
-  filter_by_gene_symbol: set to 1 if filter by gene symbol.
-                         Do not set if filtering by HGNC_id.
-                         This option is set to 1 when using PanelApp files. 
+  filter_by_gene_symbol : set to 1 if filter by gene symbol.
+                          Do not set if filtering by HGNC_id.
+                          This option is set to 1 when using PanelApp files. 
 
   only_mane            : set to 1 to ignore transcripts that are not MANE
                          N/B - Information may be lost if this option is used.
 
  For more information - https://www.ebi.ac.uk/gene2phenotype/g2p_vep_plugin
+
  Example:
-
  --plugin G2P,file=G2P.csv,af_monoallelic=0.05,types=stop_gained&frameshift_variant
  --plugin G2P,file=G2P.csv,af_monoallelic=0.05,af_from_vcf=1
  --plugin G2P,file=G2P.csv,af_from_vcf=1,af_from_vcf_keys='topmed&gnomADe_r2.1.1'

GeneSplicer.pm

@@ -60,15 +60,16 @@ limitations under the License.
 
  Example: diff/donor/621915-621914/Medium-Medium/7.020731-6.988368
 
- Several parameters can be modified by passing them to the plugin string:
+ Several key=value parameters can be modified in the the plugin string:
 
  context    : change the amount of sequence added either side of
               the variant (default: 100bp)
  tmpdir     : change the temporary directory used (default: /tmp)
  cache_size : change how many sequences' scores are cached in memory
               (default: 50)
 
- Example: --plugin GeneSplicer,$GS/bin/linux/genesplicer,$GS/human,context=200,tmpdir=/mytmp
+ Example:
+   --plugin GeneSplicer,$GS/bin/linux/genesplicer,$GS/human,context=200,tmpdir=/mytmp
 
  On some systems the binaries provided will not execute, but can be compiled from source:
 

Geno2MP.pm

@@ -42,11 +42,11 @@ limitations under the License.
  rare variant genotypes linked to phenotypic information.
 
  Parameters can be set using a key=value system:
-   file: VCF file containing Geno2MP data
-   cols: colon-delimited list of Geno2MP columns to return from INFO fields
-         (by default it only returns the column HPO_CT)
-   url: build and return URL to Geno2MP variant page (boolean; 0 by default);
-        the variant location in Geno2MP website is based on GRCh37 coordinates
+   file : VCF file containing Geno2MP data
+   cols : colon-delimited list of Geno2MP columns to return from INFO fields
+          (by default it only returns the column HPO_CT)
+   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:
  Geno2MP, NHGRI/NHLBI University of Washington-Center for Mendelian Genomics (UW-CMG), Seattle, WA

IntAct.pm

@@ -56,23 +56,23 @@ limitations under the License.
 
  Options are passed to the plugin as key=value pairs:
 
- mapping_file			: (mandatory) Path to tabix-indexed genomic location mapped file
- mutation_file			: (mandatory) Path to IntAct data file
+ mapping_file     : (mandatory) Path to tabix-indexed genomic location mapped file
+ mutation_file    : (mandatory) Path to IntAct data file
 
- By default the output will always contain feature_type and interaction_ac from the IntAct data file. You can also add more fields using the following options -
- feature_ac			: Set value to 1 to include Feature AC in the output
- feature_short_label		: Set value to 1 to include Feature short label in the output
- feature_annotation		: Set value to 1 to include Feature annotation in the output
- ap_ac				: Set value to 1 to include Affected protein AC in the output
- interaction_participants	: Set value to 1 to include Interaction participants in the output
- pmid				: Set value to 1 to include PubMedID in the output
-
- There are also two other options for customizing the output - 
- all                            : Set value to 1 to include all the fields
- minimal                        : Set value to 1 to overwrite default behavior and include only interaction_ac 
+ By default the output will always contain feature_type and interaction_ac from the IntAct data file. You can also add more fields using the following key=value options -
+   feature_ac               : Set value to 1 to include Feature AC in the output
+   feature_short_label      : Set value to 1 to include Feature short label in the output
+   feature_annotation       : Set value to 1 to include Feature annotation in the output
+   ap_ac                    : Set value to 1 to include Affected protein AC in the output
+   interaction_participants : Set value to 1 to include Interaction participants in the output
+   pmid                     : Set value to 1 to include PubMedID in the output
+
+ There are also two other key=value options for customizing the output - 
+   all     : Set value to 1 to include all the fields
+   minimal : Set value to 1 to overwrite default behavior and include only interaction_ac 
 				  in the output by default
 
- See what this options mean - https://www.ebi.ac.uk/intact/download/datasets#mutations
+ 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 :