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@@ -8,7 +8,7 @@ my $VEP_PLUGIN_CONFIG = { |
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# https://github.com/ensembl-variation/VEP_plugins/blob/master/dbNSFP.pm
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# Requires tabix-indexed data file as first param
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# Field names are listed below and rendered as a multi-selectable autocomplete text field
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- # Human, GRCh38 only
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+ # Human, GRCh38 only (3.x), for GRCh37 use 2.9.x
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{
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"key" => "dbNSFP",
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"label" => "dbNSFP",
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@@ -20,7 +20,7 @@ my $VEP_PLUGIN_CONFIG = { |
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"requires_data" => 1,
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"requires_install" => 1,
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"params" => [
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- #"/path/to/dbNSFP3.2a.txt.gz",
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+ #"/path/to/dbNSFP3.4a.txt.gz",
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"@*"
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],
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"species" => [
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@@ -36,7 +36,7 @@ my $VEP_PLUGIN_CONFIG = { |
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'multiple' => 1,
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'style' => 'height:150px',
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'required' => 1,
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- 'notes' => 'Field descriptions in <a rel="external" href="https://drive.google.com/file/d/0B60wROKy6OqcUl9NbkFRdVZlQzQ/view">dbNSFP README</a>',
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+ 'notes' => 'Field descriptions in <a rel="external" href="https://drive.google.com/file/d/0B60wROKy6OqcanRNcTZsWmxyNTA/view">dbNSFP README</a>',
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# "class" => "jquery-multiselect",
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"values" => [
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# "chr",
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@@ -45,7 +45,7 @@ my $VEP_PLUGIN_CONFIG = { |
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# "alt",
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# "aaref",
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# "aaalt",
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- # "rs_dbSNP146",
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+ # "rs_dbSNP147",
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# "hg19_chr",
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# "hg19_pos(1-based)",
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# "hg18_chr",
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@@ -62,18 +62,18 @@ my $VEP_PLUGIN_CONFIG = { |
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# "Ensembl_transcriptid",
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# "Ensembl_proteinid",
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# "aapos",
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- #"SIFT_score",
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- #"SIFT_converted_rankscore",
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- #"SIFT_pred",
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+ # "SIFT_score",
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+ # "SIFT_converted_rankscore",
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+ # "SIFT_pred",
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# "Uniprot_acc_Polyphen2",
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# "Uniprot_id_Polyphen2",
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# "Uniprot_aapos_Polyphen2",
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- #"Polyphen2_HDIV_score",
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- #"Polyphen2_HDIV_rankscore",
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- #"Polyphen2_HDIV_pred",
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- #"Polyphen2_HVAR_score",
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- #"Polyphen2_HVAR_rankscore",
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- #"Polyphen2_HVAR_pred",
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+ # "Polyphen2_HDIV_score",
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+ # "Polyphen2_HDIV_rankscore",
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+ # "Polyphen2_HDIV_pred",
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+ # "Polyphen2_HVAR_score",
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+ # "Polyphen2_HVAR_rankscore",
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+ # "Polyphen2_HVAR_pred",
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"LRT_score",
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"LRT_converted_rankscore",
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"LRT_pred",
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@@ -105,6 +105,16 @@ my $VEP_PLUGIN_CONFIG = { |
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"MetaLR_rankscore",
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"MetaLR_pred",
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"Reliability_index",
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+ "M-CAP_score",
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+ "M-CAP_rankscore",
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+ "M-CAP_pred",
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+ "REVEL_score",
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+ "REVEL_rankscore",
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+ "MutPred_score",
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+ "MutPred_rankscore",
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+ "MutPred_protID",
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+ "MutPred_AAchange",
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+ "MutPred_Top5features",
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"CADD_raw",
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"CADD_raw_rankscore",
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"CADD_phred",
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@@ -114,10 +124,11 @@ my $VEP_PLUGIN_CONFIG = { |
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"fathmm-MKL_coding_rankscore",
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"fathmm-MKL_coding_pred",
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"fathmm-MKL_coding_group",
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+ "Eigen_coding_or_noncoding",
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"Eigen-raw",
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"Eigen-phred",
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- "Eigen-raw_rankscore",
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"Eigen-PC-raw",
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+ "Eigen-PC-phred",
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"Eigen-PC-raw_rankscore",
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"GenoCanyon_score",
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"GenoCanyon_score_rankscore",
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@@ -221,7 +232,7 @@ my $VEP_PLUGIN_CONFIG = { |
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"clinvar_golden_stars",
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# "Interpro_domain",
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"GTEx_V6_gene",
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- "GTEx_V6_tissue"
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+ "GTEx_V6_tissue",
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],
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},
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]
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willmclaren
committed
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4b5d3b1