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add more plugins
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William McLaren committed Jul 9, 2015
1 parent f246f3d commit 5f6b43f
Showing 1 changed file with 167 additions and 3 deletions.
170 changes: 167 additions & 3 deletions plugin_config.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -159,6 +159,25 @@ my $VEP_PLUGIN_CONFIG = {
]
},

# dbscSNV
{
"key" => "dbscSNV",
"label" => "dbscSNV",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "Retrieves data for splicing variants from a tabix-indexed dbscSNV file",
"plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/dbscSNV.pm",
"requires_data" => 1,
"requires_install" => 1,
"params" => [
#"/path/to/dbscSNV.txt.gz"
],
"species" => [
"homo_sapiens"
],
},

# CADD
# https://github.com/ensembl-variation/VEP_plugins/blob/master/CADD.pm
# Requires tabix-indexed data file as first param
Expand Down Expand Up @@ -267,6 +286,22 @@ my $VEP_PLUGIN_CONFIG = {
],
},

# LOFTEE
# Requires LoFtool_scores.txt file as first param (available in VEP_plugins GitHub repo)
{
"key" => "LoF",
"helptip" => "Identify LoF (loss-of-function) variation",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/konradjk/loftee/master/LoF.pm",
"requires_data" => 1,
"requires_install" => 1,
"params" => [
"@*"
]
},

# LoFtool
# Requires LoFtool_scores.txt file as first param (available in VEP_plugins GitHub repo)
{
Expand Down Expand Up @@ -372,8 +407,8 @@ my $VEP_PLUGIN_CONFIG = {
},


## OTHER
########
## VARIANT DATA
###############

# ExAC
{
Expand All @@ -382,6 +417,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 1,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/ExAC.pm",
"section" => "Variant data",
"requires_data" => 1,
"species" => [
"homo_sapiens"
Expand All @@ -391,6 +427,103 @@ my $VEP_PLUGIN_CONFIG = {
]
},

# LD
{
"key" => "LD",
"label" => "Linkage disequilibrium",
"helptip" => "Finds variants in linkage disequilibrium with any overlapping existing variants from the Ensembl variation databases",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/LD.pm",
"section" => "Variant data",
"params" => [
"@*"
],
"form" => [
{
"name" => "population",
"label" => "Population",
"type" => "dropdown",
"values" => [
{ "value" => "1000GENOMES:phase_3:ACB", "caption" => "African Caribbean in Barbados" },
{ "value" => "1000GENOMES:phase_3:ASW", "caption" => "African Ancestry in Southwest US" },
{ "value" => "1000GENOMES:phase_3:BEB", "caption" => "Bengali in Bangladesh" },
{ "value" => "1000GENOMES:phase_3:CDX", "caption" => "Chinese Dai in Xishuangbanna, China" },
{ "value" => "1000GENOMES:phase_3:CEU", "caption" => "Utah residents with Northern and Western European ancestry" },
{ "value" => "1000GENOMES:phase_3:CHB", "caption" => "Han Chinese in Bejing, China" },
{ "value" => "1000GENOMES:phase_3:CHS", "caption" => "Southern Han Chinese, China" },
{ "value" => "1000GENOMES:phase_3:CLM", "caption" => "Colombian in Medellin, Colombia" },
{ "value" => "1000GENOMES:phase_3:ESN", "caption" => "Esan in Nigeria" },
{ "value" => "1000GENOMES:phase_3:FIN", "caption" => "Finnish in Finland" },
{ "value" => "1000GENOMES:phase_3:GBR", "caption" => "British in England and Scotland" },
{ "value" => "1000GENOMES:phase_3:GIH", "caption" => "Gujarati Indian in Houston, TX" },
{ "value" => "1000GENOMES:phase_3:IBS", "caption" => "Iberian populations in Spain" },
{ "value" => "1000GENOMES:phase_3:ITU", "caption" => "Indian Telugu in the UK" },
{ "value" => "1000GENOMES:phase_3:JPT", "caption" => "Japanese in Tokyo, Japan" },
{ "value" => "1000GENOMES:phase_3:KHV", "caption" => "Kinh in Ho Chi Minh City, Vietnam" },
{ "value" => "1000GENOMES:phase_3:LWK", "caption" => "Luhya in Webuye, Kenya" },
{ "value" => "1000GENOMES:phase_3:MAG", "caption" => "Mandinka in The Gambia" },
{ "value" => "1000GENOMES:phase_3:MSL", "caption" => "Mende in Sierra Leone" },
{ "value" => "1000GENOMES:phase_3:MXL", "caption" => "Mexican Ancestry in Los Angeles, California" },
{ "value" => "1000GENOMES:phase_3:PEL", "caption" => "Peruvian in Lima, Peru" },
{ "value" => "1000GENOMES:phase_3:PJL", "caption" => "Punjabi in Lahore, Pakistan" },
{ "value" => "1000GENOMES:phase_3:PUR", "caption" => "Puerto Rican in Puerto Rico" },
{ "value" => "1000GENOMES:phase_3:STU", "caption" => "Sri Lankan Tamil in the UK" },
{ "value" => "1000GENOMES:phase_3:TSI", "caption" => "Toscani in Italy" },
{ "value" => "1000GENOMES:phase_3:YRI", "caption" => "Yoruba in Ibadan, Nigeria" },
],
"value" => "1000GENOMES:phase_3:CEU",
},
{
"name" => "threshold",
"label" => "r2 cutoff",
"type" => "string",
"value" => 0.8,
},
]
},

# SameCodon
{
"key" => "SameCodon",
"label" => "Variants in same codon",
"helptip" => "Reports existing variants that fall in the same codon",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/SameCodon.pm",
"section" => "Variant data",
},


## GENE/TRANSCRIPT DATA
#######################

# GO
{
"key" => "GO",
"label" => "Gene Ontology",
"helptip" => "Retrieves Gene Ontology terms associated with transcripts/translations via the Ensembl API",
"available" => 1,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/GO.pm",
"section" => "Gene data",
},

# GXA
{
"key" => "GXA",
"label" => "Gene Expression Atlas",
"helptip" => "Reports data from the Gene Expression Atlas",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/GXA.pm",
"section" => "Gene data",
},


## OTHER
########

# miRNA
{
"key" => "miRNA",
Expand All @@ -399,7 +532,8 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 1,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/miRNA.pm",
},
},


# UpDownDistance
# https://github.com/ensembl-variation/VEP_plugins/blob/master/UpDownDistance.pm
Expand All @@ -423,5 +557,35 @@ my $VEP_PLUGIN_CONFIG = {
}
]
},

# Downstream
{
"key" => "Downstream",
"label" => "Downstream",
"helptip" => "Predicts the downstream effects of a frameshift variant on the protein sequence of a transcript",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/Downstream.pm",
},

# ProteinSeqs
{
"key" => "ProteinSeqs",
"label" => "Protein sequences",
"helptip" => "Prints out the reference and mutated protein sequences of any proteins found with non-synonymous mutations",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/ProteinSeqs.pm",
},

# TSSDistance
{
"key" => "TSSDistance",
"label" => "TSS distance",
"helptip" => "Calculates the distance from the transcription start site for upstream variants ",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/TSSDistance.pm",
},
]
};

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