From 4b5d3b12109fa0092ae62aff290d83739c5590b7 Mon Sep 17 00:00:00 2001
From: William McLaren <wm2@ebi.ac.uk>
Date: Thu, 25 May 2017 15:37:07 +0100
Subject: [PATCH] update fields for dbNSFP3.4a

---
 plugin_config.txt | 41 ++++++++++++++++++++++++++---------------
 1 file changed, 26 insertions(+), 15 deletions(-)

diff --git a/plugin_config.txt b/plugin_config.txt
index 95fc79a..bf8d32a 100644
--- a/plugin_config.txt
+++ b/plugin_config.txt
@@ -8,7 +8,7 @@ my $VEP_PLUGIN_CONFIG = {
     # https://github.com/ensembl-variation/VEP_plugins/blob/master/dbNSFP.pm
     # Requires tabix-indexed data file as first param
     # Field names are listed below and rendered as a multi-selectable autocomplete text field
-    # Human, GRCh38 only
+    # Human, GRCh38 only (3.x), for GRCh37 use 2.9.x
     {
       "key" => "dbNSFP",
       "label" => "dbNSFP",
@@ -20,7 +20,7 @@ my $VEP_PLUGIN_CONFIG = {
       "requires_data" => 1,
       "requires_install" => 1,
       "params"  => [
-        #"/path/to/dbNSFP3.2a.txt.gz",
+        #"/path/to/dbNSFP3.4a.txt.gz",
         "@*"
       ],
       "species" => [
@@ -36,7 +36,7 @@ my $VEP_PLUGIN_CONFIG = {
           'multiple' => 1,
           'style' => 'height:150px',
           'required' => 1,
-          'notes' => 'Field descriptions in <a rel="external" href="https://drive.google.com/file/d/0B60wROKy6OqcUl9NbkFRdVZlQzQ/view">dbNSFP README</a>',
+          'notes' => 'Field descriptions in <a rel="external" href="https://drive.google.com/file/d/0B60wROKy6OqcanRNcTZsWmxyNTA/view">dbNSFP README</a>',
           # "class" => "jquery-multiselect",
           "values" => [
             # "chr",
@@ -45,7 +45,7 @@ my $VEP_PLUGIN_CONFIG = {
             # "alt",
             # "aaref",
             # "aaalt",
-            # "rs_dbSNP146",
+            # "rs_dbSNP147",
             # "hg19_chr",
             # "hg19_pos(1-based)",
             # "hg18_chr",
@@ -62,18 +62,18 @@ my $VEP_PLUGIN_CONFIG = {
             # "Ensembl_transcriptid",
             # "Ensembl_proteinid",
             # "aapos",
-            #"SIFT_score",
-            #"SIFT_converted_rankscore",
-            #"SIFT_pred",
+            # "SIFT_score",
+            # "SIFT_converted_rankscore",
+            # "SIFT_pred",
             # "Uniprot_acc_Polyphen2",
             # "Uniprot_id_Polyphen2",
             # "Uniprot_aapos_Polyphen2",
-            #"Polyphen2_HDIV_score",
-            #"Polyphen2_HDIV_rankscore",
-            #"Polyphen2_HDIV_pred",
-            #"Polyphen2_HVAR_score",
-            #"Polyphen2_HVAR_rankscore",
-            #"Polyphen2_HVAR_pred",
+            # "Polyphen2_HDIV_score",
+            # "Polyphen2_HDIV_rankscore",
+            # "Polyphen2_HDIV_pred",
+            # "Polyphen2_HVAR_score",
+            # "Polyphen2_HVAR_rankscore",
+            # "Polyphen2_HVAR_pred",
             "LRT_score",
             "LRT_converted_rankscore",
             "LRT_pred",
@@ -105,6 +105,16 @@ my $VEP_PLUGIN_CONFIG = {
             "MetaLR_rankscore",
             "MetaLR_pred",
             "Reliability_index",
+            "M-CAP_score",
+            "M-CAP_rankscore",
+            "M-CAP_pred",
+            "REVEL_score",
+            "REVEL_rankscore",
+            "MutPred_score",
+            "MutPred_rankscore",
+            "MutPred_protID",
+            "MutPred_AAchange",
+            "MutPred_Top5features",
             "CADD_raw",
             "CADD_raw_rankscore",
             "CADD_phred",
@@ -114,10 +124,11 @@ my $VEP_PLUGIN_CONFIG = {
             "fathmm-MKL_coding_rankscore",
             "fathmm-MKL_coding_pred",
             "fathmm-MKL_coding_group",
+            "Eigen_coding_or_noncoding",
             "Eigen-raw",
             "Eigen-phred",
-            "Eigen-raw_rankscore",
             "Eigen-PC-raw",
+            "Eigen-PC-phred",
             "Eigen-PC-raw_rankscore",
             "GenoCanyon_score",
             "GenoCanyon_score_rankscore",
@@ -221,7 +232,7 @@ my $VEP_PLUGIN_CONFIG = {
             "clinvar_golden_stars",
             # "Interpro_domain",
             "GTEx_V6_gene",
-            "GTEx_V6_tissue"
+            "GTEx_V6_tissue",
           ],
         },
       ]