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plugin_config.txt
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plugin_config.txt
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my $VEP_PLUGIN_CONFIG = {
"plugins" => [
## PATHOGENICITY PREDICTIONS
############################
# dbNSFP
# https://github.com/ensembl-variation/VEP_plugins/blob/main/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 (3.x), for GRCh37 use 2.9.x
{
"key" => "dbNSFP",
"label" => "dbNSFP",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "dbNSFP provides pathogenicity predictions for missense variants from various algorithms",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/112/dbNSFP.pm",
"requires_data" => 1,
"requires_install" => 1,
"params" => [
#"/path/to/dbNSFP4.5c_grch38.gz",
"@*"
],
"species" => [
"homo_sapiens"
],
"form" => [
{
"name" => "dbNSFP_fields",
"label" => "Fields to include",
"helptip" => "Fields to fetch from dbNSFP; hold down the Ctrl (Windows) / Command (Mac) button to select multiple options",
"value" => "",
'type' => 'dropdown',
'multiple' => 1,
'style' => 'height:150px',
'required' => 1,
'notes' => 'Field descriptions in <a rel="external" href="https://usf.app.box.com/s/jpg94a3t0qi529095v7wn4kpmr1at2aa">dbNSFP README</a>',
# "class" => "jquery-multiselect",
"values" => [
#"#chr",
#"pos(1-based)",
#"ref",
#"alt",
#"aaref",
#"aaalt",
#"rs_dbSNP",
#"hg19_chr",
#"hg19_pos(1-based)",
#"hg18_chr",
#"hg18_pos(1-based)",
"aapos",
"genename",
"Ensembl_geneid",
"Ensembl_transcriptid",
"Ensembl_proteinid",
"Uniprot_acc",
"Uniprot_entry",
#"HGVSc_ANNOVAR",
#"HGVSp_ANNOVAR",
#"HGVSc_snpEff",
#"HGVSp_snpEff",
#"HGVSc_VEP",
#"HGVSp_VEP",
#"APPRIS",
#"GENCODE_basic",
#"TSL",
#"VEP_canonical",
#"cds_strand",
#"refcodon",
#"codonpos",
"codon_degeneracy",
"Ancestral_allele",
"AltaiNeandertal",
"Denisova",
"VindijiaNeandertal",
"ChagyrskayaNeandertal",
#"SIFT_score",
#"SIFT_converted_rankscore",
#"SIFT_pred",
#"SIFT4G_score",
#"SIFT4G_converted_rankscore",
#"SIFT4G_pred",
"LRT_score",
"LRT_converted_rankscore",
"LRT_pred",
"LRT_Omega",
"MutationTaster_score",
"MutationTaster_converted_rankscore",
"MutationTaster_pred",
"MutationTaster_model",
"MutationTaster_AAE",
"MutationAssessor_score",
"MutationAssessor_rankscore",
"MutationAssessor_pred",
"FATHMM_score",
"FATHMM_converted_rankscore",
"FATHMM_pred",
"PROVEAN_score",
"PROVEAN_converted_rankscore",
"PROVEAN_pred",
"MetaSVM_score",
"MetaSVM_rankscore",
"MetaSVM_pred",
"MetaLR_score",
"MetaLR_rankscore",
"MetaLR_pred",
"Reliability_index",
"MetaRNN_score",
"MetaRNN_rankscore",
"MetaRNN_pred",
"M-CAP_score",
"M-CAP_rankscore",
"M-CAP_pred",
"MutPred_score",
"MutPred_rankscore",
"MutPred_protID",
"MutPred_AAchange",
"MutPred_Top5features",
"MVP_score",
"MVP_rankscore",
"gMVP_score",
"gMVP_rankscore",
"MPC_score",
"MPC_rankscore",
"PrimateAI_score",
"PrimateAI_rankscore",
"PrimateAI_pred",
"DEOGEN2_score",
"DEOGEN2_rankscore",
"DEOGEN2_pred",
"BayesDel_addAF_score",
"BayesDel_addAF_rankscore",
"BayesDel_addAF_pred",
"BayesDel_noAF_score",
"BayesDel_noAF_rankscore",
"BayesDel_noAF_pred",
"LIST-S2_score",
"LIST-S2_rankscore",
"LIST-S2_pred",
"VARITY_R_score",
"VARITY_R_rankscore",
"VARITY_ER_score",
"VARITY_ER_rankscore",
"VARITY_R_LOO_score",
"VARITY_R_LOO_rankscore",
"VARITY_ER_LOO_score",
"VARITY_ER_LOO_rankscore",
"ESM1b_score",
"ESM1b_rankscore",
"ESM1b_pred",
"EVE_score",
"EVE_rankscore",
"EVE_Class10_pred",
"EVE_Class20_pred",
"EVE_Class25_pred",
"EVE_Class30_pred",
"EVE_Class40_pred",
"EVE_Class50_pred",
"EVE_Class60_pred",
"EVE_Class70_pred",
"EVE_Class75_pred",
"EVE_Class80_pred",
"EVE_Class90_pred",
"Aloft_Fraction_transcripts_affected",
"Aloft_prob_Tolerant",
"Aloft_prob_Recessive",
"Aloft_prob_Dominant",
"Aloft_pred",
"Aloft_Confidence",
"DANN_score",
"DANN_rankscore",
"fathmm-MKL_coding_score",
"fathmm-MKL_coding_rankscore",
"fathmm-MKL_coding_pred",
"fathmm-MKL_coding_group",
"fathmm-XF_coding_score",
"fathmm-XF_coding_rankscore",
"fathmm-XF_coding_pred",
"Eigen-raw_coding",
"Eigen-raw_coding_rankscore",
"Eigen-phred_coding",
"Eigen-PC-raw_coding",
"Eigen-PC-raw_coding_rankscore",
"Eigen-PC-phred_coding",
"integrated_fitCons_score",
"integrated_fitCons_rankscore",
"integrated_confidence_value",
"GM12878_fitCons_score",
"GM12878_fitCons_rankscore",
"GM12878_confidence_value",
"H1-hESC_fitCons_score",
"H1-hESC_fitCons_rankscore",
"H1-hESC_confidence_value",
"HUVEC_fitCons_score",
"HUVEC_fitCons_rankscore",
"HUVEC_confidence_value",
"GERP++_NR",
"GERP++_RS",
"GERP++_RS_rankscore",
"phyloP100way_vertebrate",
"phyloP100way_vertebrate_rankscore",
"phyloP470way_mammalian",
"phyloP470way_mammalian_rankscore",
"phyloP17way_primate",
"phyloP17way_primate_rankscore",
"phastCons100way_vertebrate",
"phastCons100way_vertebrate_rankscore",
"phastCons470way_mammalian",
"phastCons470way_mammalian_rankscore",
"phastCons17way_primate",
"phastCons17way_primate_rankscore",
"SiPhy_29way_pi",
"SiPhy_29way_logOdds",
"SiPhy_29way_logOdds_rankscore",
"bStatistic",
"bStatistic_converted_rankscore",
"1000Gp3_AC",
"1000Gp3_AF",
"1000Gp3_AFR_AC",
"1000Gp3_AFR_AF",
"1000Gp3_EUR_AC",
"1000Gp3_EUR_AF",
"1000Gp3_AMR_AC",
"1000Gp3_AMR_AF",
"1000Gp3_EAS_AC",
"1000Gp3_EAS_AF",
"1000Gp3_SAS_AC",
"1000Gp3_SAS_AF",
"TWINSUK_AC",
"TWINSUK_AF",
"ALSPAC_AC",
"ALSPAC_AF",
"UK10K_AC",
"UK10K_AF",
"ESP6500_AA_AC",
"ESP6500_AA_AF",
"ESP6500_EA_AC",
"ESP6500_EA_AF",
"ExAC_AC",
"ExAC_AF",
"ExAC_Adj_AC",
"ExAC_Adj_AF",
"ExAC_AFR_AC",
"ExAC_AFR_AF",
"ExAC_AMR_AC",
"ExAC_AMR_AF",
"ExAC_EAS_AC",
"ExAC_EAS_AF",
"ExAC_FIN_AC",
"ExAC_FIN_AF",
"ExAC_NFE_AC",
"ExAC_NFE_AF",
"ExAC_SAS_AC",
"ExAC_SAS_AF",
"ExAC_nonTCGA_AC",
"ExAC_nonTCGA_AF",
"ExAC_nonTCGA_Adj_AC",
"ExAC_nonTCGA_Adj_AF",
"ExAC_nonTCGA_AFR_AC",
"ExAC_nonTCGA_AFR_AF",
"ExAC_nonTCGA_AMR_AC",
"ExAC_nonTCGA_AMR_AF",
"ExAC_nonTCGA_EAS_AC",
"ExAC_nonTCGA_EAS_AF",
"ExAC_nonTCGA_FIN_AC",
"ExAC_nonTCGA_FIN_AF",
"ExAC_nonTCGA_NFE_AC",
"ExAC_nonTCGA_NFE_AF",
"ExAC_nonTCGA_SAS_AC",
"ExAC_nonTCGA_SAS_AF",
"ExAC_nonpsych_AC",
"ExAC_nonpsych_AF",
"ExAC_nonpsych_Adj_AC",
"ExAC_nonpsych_Adj_AF",
"ExAC_nonpsych_AFR_AC",
"ExAC_nonpsych_AFR_AF",
"ExAC_nonpsych_AMR_AC",
"ExAC_nonpsych_AMR_AF",
"ExAC_nonpsych_EAS_AC",
"ExAC_nonpsych_EAS_AF",
"ExAC_nonpsych_FIN_AC",
"ExAC_nonpsych_FIN_AF",
"ExAC_nonpsych_NFE_AC",
"ExAC_nonpsych_NFE_AF",
"ExAC_nonpsych_SAS_AC",
"ExAC_nonpsych_SAS_AF",
"gnomAD_exomes_flag",
"gnomAD_exomes_AC",
"gnomAD_exomes_AN",
"gnomAD_exomes_AF",
"gnomAD_exomes_nhomalt",
"gnomAD_exomes_AFR_AC",
"gnomAD_exomes_AFR_AN",
"gnomAD_exomes_AFR_AF",
"gnomAD_exomes_AFR_nhomalt",
"gnomAD_exomes_AMR_AC",
"gnomAD_exomes_AMR_AN",
"gnomAD_exomes_AMR_AF",
"gnomAD_exomes_AMR_nhomalt",
"gnomAD_exomes_ASJ_AC",
"gnomAD_exomes_ASJ_AN",
"gnomAD_exomes_ASJ_AF",
"gnomAD_exomes_ASJ_nhomalt",
"gnomAD_exomes_EAS_AC",
"gnomAD_exomes_EAS_AN",
"gnomAD_exomes_EAS_AF",
"gnomAD_exomes_EAS_nhomalt",
"gnomAD_exomes_FIN_AC",
"gnomAD_exomes_FIN_AN",
"gnomAD_exomes_FIN_AF",
"gnomAD_exomes_FIN_nhomalt",
"gnomAD_exomes_NFE_AC",
"gnomAD_exomes_NFE_AN",
"gnomAD_exomes_NFE_AF",
"gnomAD_exomes_NFE_nhomalt",
"gnomAD_exomes_SAS_AC",
"gnomAD_exomes_SAS_AN",
"gnomAD_exomes_SAS_AF",
"gnomAD_exomes_SAS_nhomalt",
"gnomAD_exomes_POPMAX_AC",
"gnomAD_exomes_POPMAX_AN",
"gnomAD_exomes_POPMAX_AF",
"gnomAD_exomes_POPMAX_nhomalt",
"gnomAD_exomes_controls_AC",
"gnomAD_exomes_controls_AN",
"gnomAD_exomes_controls_AF",
"gnomAD_exomes_controls_nhomalt",
"gnomAD_exomes_non_neuro_AC",
"gnomAD_exomes_non_neuro_AN",
"gnomAD_exomes_non_neuro_AF",
"gnomAD_exomes_non_neuro_nhomalt",
"gnomAD_exomes_non_cancer_AC",
"gnomAD_exomes_non_cancer_AN",
"gnomAD_exomes_non_cancer_AF",
"gnomAD_exomes_non_cancer_nhomalt",
"gnomAD_exomes_non_topmed_AC",
"gnomAD_exomes_non_topmed_AN",
"gnomAD_exomes_non_topmed_AF",
"gnomAD_exomes_non_topmed_nhomalt",
"gnomAD_exomes_controls_AFR_AC",
"gnomAD_exomes_controls_AFR_AN",
"gnomAD_exomes_controls_AFR_AF",
"gnomAD_exomes_controls_AFR_nhomalt",
"gnomAD_exomes_controls_AMR_AC",
"gnomAD_exomes_controls_AMR_AN",
"gnomAD_exomes_controls_AMR_AF",
"gnomAD_exomes_controls_AMR_nhomalt",
"gnomAD_exomes_controls_ASJ_AC",
"gnomAD_exomes_controls_ASJ_AN",
"gnomAD_exomes_controls_ASJ_AF",
"gnomAD_exomes_controls_ASJ_nhomalt",
"gnomAD_exomes_controls_EAS_AC",
"gnomAD_exomes_controls_EAS_AN",
"gnomAD_exomes_controls_EAS_AF",
"gnomAD_exomes_controls_EAS_nhomalt",
"gnomAD_exomes_controls_FIN_AC",
"gnomAD_exomes_controls_FIN_AN",
"gnomAD_exomes_controls_FIN_AF",
"gnomAD_exomes_controls_FIN_nhomalt",
"gnomAD_exomes_controls_NFE_AC",
"gnomAD_exomes_controls_NFE_AN",
"gnomAD_exomes_controls_NFE_AF",
"gnomAD_exomes_controls_NFE_nhomalt",
"gnomAD_exomes_controls_SAS_AC",
"gnomAD_exomes_controls_SAS_AN",
"gnomAD_exomes_controls_SAS_AF",
"gnomAD_exomes_controls_SAS_nhomalt",
"gnomAD_exomes_controls_POPMAX_AC",
"gnomAD_exomes_controls_POPMAX_AN",
"gnomAD_exomes_controls_POPMAX_AF",
"gnomAD_exomes_controls_POPMAX_nhomalt",
"gnomAD_exomes_non_neuro_AFR_AC",
"gnomAD_exomes_non_neuro_AFR_AN",
"gnomAD_exomes_non_neuro_AFR_AF",
"gnomAD_exomes_non_neuro_AFR_nhomalt",
"gnomAD_exomes_non_neuro_AMR_AC",
"gnomAD_exomes_non_neuro_AMR_AN",
"gnomAD_exomes_non_neuro_AMR_AF",
"gnomAD_exomes_non_neuro_AMR_nhomalt",
"gnomAD_exomes_non_neuro_ASJ_AC",
"gnomAD_exomes_non_neuro_ASJ_AN",
"gnomAD_exomes_non_neuro_ASJ_AF",
"gnomAD_exomes_non_neuro_ASJ_nhomalt",
"gnomAD_exomes_non_neuro_EAS_AC",
"gnomAD_exomes_non_neuro_EAS_AN",
"gnomAD_exomes_non_neuro_EAS_AF",
"gnomAD_exomes_non_neuro_EAS_nhomalt",
"gnomAD_exomes_non_neuro_FIN_AC",
"gnomAD_exomes_non_neuro_FIN_AN",
"gnomAD_exomes_non_neuro_FIN_AF",
"gnomAD_exomes_non_neuro_FIN_nhomalt",
"gnomAD_exomes_non_neuro_NFE_AC",
"gnomAD_exomes_non_neuro_NFE_AN",
"gnomAD_exomes_non_neuro_NFE_AF",
"gnomAD_exomes_non_neuro_NFE_nhomalt",
"gnomAD_exomes_non_neuro_SAS_AC",
"gnomAD_exomes_non_neuro_SAS_AN",
"gnomAD_exomes_non_neuro_SAS_AF",
"gnomAD_exomes_non_neuro_SAS_nhomalt",
"gnomAD_exomes_non_neuro_POPMAX_AC",
"gnomAD_exomes_non_neuro_POPMAX_AN",
"gnomAD_exomes_non_neuro_POPMAX_AF",
"gnomAD_exomes_non_neuro_POPMAX_nhomalt",
"gnomAD_exomes_non_cancer_AFR_AC",
"gnomAD_exomes_non_cancer_AFR_AN",
"gnomAD_exomes_non_cancer_AFR_AF",
"gnomAD_exomes_non_cancer_AFR_nhomalt",
"gnomAD_exomes_non_cancer_AMR_AC",
"gnomAD_exomes_non_cancer_AMR_AN",
"gnomAD_exomes_non_cancer_AMR_AF",
"gnomAD_exomes_non_cancer_AMR_nhomalt",
"gnomAD_exomes_non_cancer_ASJ_AC",
"gnomAD_exomes_non_cancer_ASJ_AN",
"gnomAD_exomes_non_cancer_ASJ_AF",
"gnomAD_exomes_non_cancer_ASJ_nhomalt",
"gnomAD_exomes_non_cancer_EAS_AC",
"gnomAD_exomes_non_cancer_EAS_AN",
"gnomAD_exomes_non_cancer_EAS_AF",
"gnomAD_exomes_non_cancer_EAS_nhomalt",
"gnomAD_exomes_non_cancer_FIN_AC",
"gnomAD_exomes_non_cancer_FIN_AN",
"gnomAD_exomes_non_cancer_FIN_AF",
"gnomAD_exomes_non_cancer_FIN_nhomalt",
"gnomAD_exomes_non_cancer_NFE_AC",
"gnomAD_exomes_non_cancer_NFE_AN",
"gnomAD_exomes_non_cancer_NFE_AF",
"gnomAD_exomes_non_cancer_NFE_nhomalt",
"gnomAD_exomes_non_cancer_SAS_AC",
"gnomAD_exomes_non_cancer_SAS_AN",
"gnomAD_exomes_non_cancer_SAS_AF",
"gnomAD_exomes_non_cancer_SAS_nhomalt",
"gnomAD_exomes_non_cancer_POPMAX_AC",
"gnomAD_exomes_non_cancer_POPMAX_AN",
"gnomAD_exomes_non_cancer_POPMAX_AF",
"gnomAD_exomes_non_cancer_POPMAX_nhomalt",
"gnomAD_exomes_non_topmed_AFR_AC",
"gnomAD_exomes_non_topmed_AFR_AN",
"gnomAD_exomes_non_topmed_AFR_AF",
"gnomAD_exomes_non_topmed_AFR_nhomalt",
"gnomAD_exomes_non_topmed_AMR_AC",
"gnomAD_exomes_non_topmed_AMR_AN",
"gnomAD_exomes_non_topmed_AMR_AF",
"gnomAD_exomes_non_topmed_AMR_nhomalt",
"gnomAD_exomes_non_topmed_ASJ_AC",
"gnomAD_exomes_non_topmed_ASJ_AN",
"gnomAD_exomes_non_topmed_ASJ_AF",
"gnomAD_exomes_non_topmed_ASJ_nhomalt",
"gnomAD_exomes_non_topmed_EAS_AC",
"gnomAD_exomes_non_topmed_EAS_AN",
"gnomAD_exomes_non_topmed_EAS_AF",
"gnomAD_exomes_non_topmed_EAS_nhomalt",
"gnomAD_exomes_non_topmed_FIN_AC",
"gnomAD_exomes_non_topmed_FIN_AN",
"gnomAD_exomes_non_topmed_FIN_AF",
"gnomAD_exomes_non_topmed_FIN_nhomalt",
"gnomAD_exomes_non_topmed_NFE_AC",
"gnomAD_exomes_non_topmed_NFE_AN",
"gnomAD_exomes_non_topmed_NFE_AF",
"gnomAD_exomes_non_topmed_NFE_nhomalt",
"gnomAD_exomes_non_topmed_SAS_AC",
"gnomAD_exomes_non_topmed_SAS_AN",
"gnomAD_exomes_non_topmed_SAS_AF",
"gnomAD_exomes_non_topmed_SAS_nhomalt",
"gnomAD_exomes_non_topmed_POPMAX_AC",
"gnomAD_exomes_non_topmed_POPMAX_AN",
"gnomAD_exomes_non_topmed_POPMAX_AF",
"gnomAD_exomes_non_topmed_POPMAX_nhomalt",
"gnomAD_genomes_flag",
"gnomAD_genomes_AC",
"gnomAD_genomes_AN",
"gnomAD_genomes_AF",
"gnomAD_genomes_nhomalt",
"gnomAD_genomes_POPMAX_AC",
"gnomAD_genomes_POPMAX_AN",
"gnomAD_genomes_POPMAX_AF",
"gnomAD_genomes_POPMAX_nhomalt",
"gnomAD_genomes_AFR_AC",
"gnomAD_genomes_AFR_AN",
"gnomAD_genomes_AFR_AF",
"gnomAD_genomes_AFR_nhomalt",
"gnomAD_genomes_AMI_AC",
"gnomAD_genomes_AMI_AN",
"gnomAD_genomes_AMI_AF",
"gnomAD_genomes_AMI_nhomalt",
"gnomAD_genomes_AMR_AC",
"gnomAD_genomes_AMR_AN",
"gnomAD_genomes_AMR_AF",
"gnomAD_genomes_AMR_nhomalt",
"gnomAD_genomes_ASJ_AC",
"gnomAD_genomes_ASJ_AN",
"gnomAD_genomes_ASJ_AF",
"gnomAD_genomes_ASJ_nhomalt",
"gnomAD_genomes_EAS_AC",
"gnomAD_genomes_EAS_AN",
"gnomAD_genomes_EAS_AF",
"gnomAD_genomes_EAS_nhomalt",
"gnomAD_genomes_FIN_AC",
"gnomAD_genomes_FIN_AN",
"gnomAD_genomes_FIN_AF",
"gnomAD_genomes_FIN_nhomalt",
"gnomAD_genomes_MID_AC",
"gnomAD_genomes_MID_AN",
"gnomAD_genomes_MID_AF",
"gnomAD_genomes_MID_nhomalt",
"gnomAD_genomes_NFE_AC",
"gnomAD_genomes_NFE_AN",
"gnomAD_genomes_NFE_AF",
"gnomAD_genomes_NFE_nhomalt",
"gnomAD_genomes_SAS_AC",
"gnomAD_genomes_SAS_AN",
"gnomAD_genomes_SAS_AF",
"gnomAD_genomes_SAS_nhomalt",
"gnomAD_genomes_controls_and_biobanks_AC",
"gnomAD_genomes_controls_and_biobanks_AN",
"gnomAD_genomes_controls_and_biobanks_AF",
"gnomAD_genomes_controls_and_biobanks_nhomalt",
"gnomAD_genomes_non_neuro_AC",
"gnomAD_genomes_non_neuro_AN",
"gnomAD_genomes_non_neuro_AF",
"gnomAD_genomes_non_neuro_nhomalt",
"gnomAD_genomes_non_cancer_AC",
"gnomAD_genomes_non_cancer_AN",
"gnomAD_genomes_non_cancer_AF",
"gnomAD_genomes_non_cancer_nhomalt",
"gnomAD_genomes_non_topmed_AC",
"gnomAD_genomes_non_topmed_AN",
"gnomAD_genomes_non_topmed_AF",
"gnomAD_genomes_non_topmed_nhomalt",
"gnomAD_genomes_controls_and_biobanks_AFR_AC",
"gnomAD_genomes_controls_and_biobanks_AFR_AN",
"gnomAD_genomes_controls_and_biobanks_AFR_AF",
"gnomAD_genomes_controls_and_biobanks_AFR_nhomalt",
"gnomAD_genomes_controls_and_biobanks_AMI_AC",
"gnomAD_genomes_controls_and_biobanks_AMI_AN",
"gnomAD_genomes_controls_and_biobanks_AMI_AF",
"gnomAD_genomes_controls_and_biobanks_AMI_nhomalt",
"gnomAD_genomes_controls_and_biobanks_AMR_AC",
"gnomAD_genomes_controls_and_biobanks_AMR_AN",
"gnomAD_genomes_controls_and_biobanks_AMR_AF",
"gnomAD_genomes_controls_and_biobanks_AMR_nhomalt",
"gnomAD_genomes_controls_and_biobanks_ASJ_AC",
"gnomAD_genomes_controls_and_biobanks_ASJ_AN",
"gnomAD_genomes_controls_and_biobanks_ASJ_AF",
"gnomAD_genomes_controls_and_biobanks_ASJ_nhomalt",
"gnomAD_genomes_controls_and_biobanks_EAS_AC",
"gnomAD_genomes_controls_and_biobanks_EAS_AN",
"gnomAD_genomes_controls_and_biobanks_EAS_AF",
"gnomAD_genomes_controls_and_biobanks_EAS_nhomalt",
"gnomAD_genomes_controls_and_biobanks_FIN_AC",
"gnomAD_genomes_controls_and_biobanks_FIN_AN",
"gnomAD_genomes_controls_and_biobanks_FIN_AF",
"gnomAD_genomes_controls_and_biobanks_FIN_nhomalt",
"gnomAD_genomes_controls_and_biobanks_MID_AC",
"gnomAD_genomes_controls_and_biobanks_MID_AN",
"gnomAD_genomes_controls_and_biobanks_MID_AF",
"gnomAD_genomes_controls_and_biobanks_MID_nhomalt",
"gnomAD_genomes_controls_and_biobanks_NFE_AC",
"gnomAD_genomes_controls_and_biobanks_NFE_AN",
"gnomAD_genomes_controls_and_biobanks_NFE_AF",
"gnomAD_genomes_controls_and_biobanks_NFE_nhomalt",
"gnomAD_genomes_controls_and_biobanks_SAS_AC",
"gnomAD_genomes_controls_and_biobanks_SAS_AN",
"gnomAD_genomes_controls_and_biobanks_SAS_AF",
"gnomAD_genomes_controls_and_biobanks_SAS_nhomalt",
"gnomAD_genomes_non_neuro_AFR_AC",
"gnomAD_genomes_non_neuro_AFR_AN",
"gnomAD_genomes_non_neuro_AFR_AF",
"gnomAD_genomes_non_neuro_AFR_nhomalt",
"gnomAD_genomes_non_neuro_AMI_AC",
"gnomAD_genomes_non_neuro_AMI_AN",
"gnomAD_genomes_non_neuro_AMI_AF",
"gnomAD_genomes_non_neuro_AMI_nhomalt",
"gnomAD_genomes_non_neuro_AMR_AC",
"gnomAD_genomes_non_neuro_AMR_AN",
"gnomAD_genomes_non_neuro_AMR_AF",
"gnomAD_genomes_non_neuro_AMR_nhomalt",
"gnomAD_genomes_non_neuro_ASJ_AC",
"gnomAD_genomes_non_neuro_ASJ_AN",
"gnomAD_genomes_non_neuro_ASJ_AF",
"gnomAD_genomes_non_neuro_ASJ_nhomalt",
"gnomAD_genomes_non_neuro_EAS_AC",
"gnomAD_genomes_non_neuro_EAS_AN",
"gnomAD_genomes_non_neuro_EAS_AF",
"gnomAD_genomes_non_neuro_EAS_nhomalt",
"gnomAD_genomes_non_neuro_FIN_AC",
"gnomAD_genomes_non_neuro_FIN_AN",
"gnomAD_genomes_non_neuro_FIN_AF",
"gnomAD_genomes_non_neuro_FIN_nhomalt",
"gnomAD_genomes_non_neuro_MID_AC",
"gnomAD_genomes_non_neuro_MID_AN",
"gnomAD_genomes_non_neuro_MID_AF",
"gnomAD_genomes_non_neuro_MID_nhomalt",
"gnomAD_genomes_non_neuro_NFE_AC",
"gnomAD_genomes_non_neuro_NFE_AN",
"gnomAD_genomes_non_neuro_NFE_AF",
"gnomAD_genomes_non_neuro_NFE_nhomalt",
"gnomAD_genomes_non_neuro_SAS_AC",
"gnomAD_genomes_non_neuro_SAS_AN",
"gnomAD_genomes_non_neuro_SAS_AF",
"gnomAD_genomes_non_neuro_SAS_nhomalt",
"gnomAD_genomes_non_cancer_AFR_AC",
"gnomAD_genomes_non_cancer_AFR_AN",
"gnomAD_genomes_non_cancer_AFR_AF",
"gnomAD_genomes_non_cancer_AFR_nhomalt",
"gnomAD_genomes_non_cancer_AMI_AC",
"gnomAD_genomes_non_cancer_AMI_AN",
"gnomAD_genomes_non_cancer_AMI_AF",
"gnomAD_genomes_non_cancer_AMI_nhomalt",
"gnomAD_genomes_non_cancer_AMR_AC",
"gnomAD_genomes_non_cancer_AMR_AN",
"gnomAD_genomes_non_cancer_AMR_AF",
"gnomAD_genomes_non_cancer_AMR_nhomalt",
"gnomAD_genomes_non_cancer_ASJ_AC",
"gnomAD_genomes_non_cancer_ASJ_AN",
"gnomAD_genomes_non_cancer_ASJ_AF",
"gnomAD_genomes_non_cancer_ASJ_nhomalt",
"gnomAD_genomes_non_cancer_EAS_AC",
"gnomAD_genomes_non_cancer_EAS_AN",
"gnomAD_genomes_non_cancer_EAS_AF",
"gnomAD_genomes_non_cancer_EAS_nhomalt",
"gnomAD_genomes_non_cancer_FIN_AC",
"gnomAD_genomes_non_cancer_FIN_AN",
"gnomAD_genomes_non_cancer_FIN_AF",
"gnomAD_genomes_non_cancer_FIN_nhomalt",
"gnomAD_genomes_non_cancer_MID_AC",
"gnomAD_genomes_non_cancer_MID_AN",
"gnomAD_genomes_non_cancer_MID_AF",
"gnomAD_genomes_non_cancer_MID_nhomalt",
"gnomAD_genomes_non_cancer_NFE_AC",
"gnomAD_genomes_non_cancer_NFE_AN",
"gnomAD_genomes_non_cancer_NFE_AF",
"gnomAD_genomes_non_cancer_NFE_nhomalt",
"gnomAD_genomes_non_cancer_SAS_AC",
"gnomAD_genomes_non_cancer_SAS_AN",
"gnomAD_genomes_non_cancer_SAS_AF",
"gnomAD_genomes_non_cancer_SAS_nhomalt",
"gnomAD_genomes_non_topmed_AFR_AC",
"gnomAD_genomes_non_topmed_AFR_AN",
"gnomAD_genomes_non_topmed_AFR_AF",
"gnomAD_genomes_non_topmed_AFR_nhomalt",
"gnomAD_genomes_non_topmed_AMI_AC",
"gnomAD_genomes_non_topmed_AMI_AN",
"gnomAD_genomes_non_topmed_AMI_AF",
"gnomAD_genomes_non_topmed_AMI_nhomalt",
"gnomAD_genomes_non_topmed_AMR_AC",
"gnomAD_genomes_non_topmed_AMR_AN",
"gnomAD_genomes_non_topmed_AMR_AF",
"gnomAD_genomes_non_topmed_AMR_nhomalt",
"gnomAD_genomes_non_topmed_ASJ_AC",
"gnomAD_genomes_non_topmed_ASJ_AN",
"gnomAD_genomes_non_topmed_ASJ_AF",
"gnomAD_genomes_non_topmed_ASJ_nhomalt",
"gnomAD_genomes_non_topmed_EAS_AC",
"gnomAD_genomes_non_topmed_EAS_AN",
"gnomAD_genomes_non_topmed_EAS_AF",
"gnomAD_genomes_non_topmed_EAS_nhomalt",
"gnomAD_genomes_non_topmed_FIN_AC",
"gnomAD_genomes_non_topmed_FIN_AN",
"gnomAD_genomes_non_topmed_FIN_AF",
"gnomAD_genomes_non_topmed_FIN_nhomalt",
"gnomAD_genomes_non_topmed_MID_AC",
"gnomAD_genomes_non_topmed_MID_AN",
"gnomAD_genomes_non_topmed_MID_AF",
"gnomAD_genomes_non_topmed_MID_nhomalt",
"gnomAD_genomes_non_topmed_NFE_AC",
"gnomAD_genomes_non_topmed_NFE_AN",
"gnomAD_genomes_non_topmed_NFE_AF",
"gnomAD_genomes_non_topmed_NFE_nhomalt",
"gnomAD_genomes_non_topmed_SAS_AC",
"gnomAD_genomes_non_topmed_SAS_AN",
"gnomAD_genomes_non_topmed_SAS_AF",
"gnomAD_genomes_non_topmed_SAS_nhomalt",
"ALFA_European_AC",
"ALFA_European_AN",
"ALFA_European_AF",
"ALFA_African_Others_AC",
"ALFA_African_Others_AN",
"ALFA_African_Others_AF",
"ALFA_East_Asian_AC",
"ALFA_East_Asian_AN",
"ALFA_East_Asian_AF",
"ALFA_African_American_AC",
"ALFA_African_American_AN",
"ALFA_African_American_AF",
"ALFA_Latin_American_1_AC",
"ALFA_Latin_American_1_AN",
"ALFA_Latin_American_1_AF",
"ALFA_Latin_American_2_AC",
"ALFA_Latin_American_2_AN",
"ALFA_Latin_American_2_AF",
"ALFA_Other_Asian_AC",
"ALFA_Other_Asian_AN",
"ALFA_Other_Asian_AF",
"ALFA_South_Asian_AC",
"ALFA_South_Asian_AN",
"ALFA_South_Asian_AF",
"ALFA_Other_AC",
"ALFA_Other_AN",
"ALFA_Other_AF",
"ALFA_African_AC",
"ALFA_African_AN",
"ALFA_African_AF",
"ALFA_Asian_AC",
"ALFA_Asian_AN",
"ALFA_Asian_AF",
"ALFA_Total_AC",
"ALFA_Total_AN",
"ALFA_Total_AF",
"clinvar_id",
"clinvar_clnsig",
"clinvar_trait",
"clinvar_review",
"clinvar_hgvs",
"clinvar_var_source",
"clinvar_MedGen_id",
"clinvar_OMIM_id",
"clinvar_Orphanet_id",
"Interpro_domain",
"GTEx_V8_gene",
"GTEx_V8_tissue",
"Geuvadis_eQTL_target_gene",
],
},
{
"name" => "dbNSFP_transcript_match",
"label" => "Transcript match",
"helptip" => "By default, some dbNSFP fields contain values for all Ensembl transcripts. Select this to only return values for the matched Ensembl transcript.",
"value" => "transcript_match=1",
"type" => "checkbox",
"style" => "height:150px"
}
]
},
# AlphaMissense
{
"key" => "AlphaMissense",
"label" => "AlphaMissense",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/112/AlphaMissense.pm",
"helptip" => "Annotates missense variants with the pre-computed AlphaMissense pathogenicity scores. AlphaMissense is a deep learning model developed by Google DeepMind that predicts the pathogenicity of single nucleotide missense variants.",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"file=/path/to/AlphaMissense_hg38.tsv.gz"
]
},
# AVADA
{
"key" => "AVADA",
"label" => "AVADA",
"available" => 0,
"enabled" => 0,
"section" => "Phenotype data and citations",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/112/AVADA.pm",
},
# CADD
# https://github.com/ensembl-variation/VEP_plugins/blob/main/CADD.pm
{
"key" => "CADD",
"label" => "CADD",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "Combined Annotation Dependent Depletion (CADD) is a tool for scoring the deleteriousness of single nucleotide variants and insertion/deletion variants in the human genome. CADD integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations. CADD is only available here for non-commercial use. See CADD website for more information.",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/112/CADD.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens",
"sus_scrofa"
],
"form" => [
{
"name" => "file_type",
"label" => "Select annotation file",
"type" => "dropdown",
"helptip" => "Select type of CADD annotation file to be used. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made.",
"values" => [
{ "value" => "snv_indels", "caption" => "CADD SNVs and InDels annotation file", "class" => "_stt_Homo_sapiens" },
{ "value" => "snv", "caption" => "CADD SNVs annotation file" },
{ "value" => "indels", "caption" => "CADD InDels annotation file", "class" => "_stt_Homo_sapiens" },
{ "value" => "sv", "caption" => "CADD-SV annotation file (supported only in GRCh38)", "class" => "_stt_Homo_sapiens" }
],
"value" => "snv_indels",
},
],
"params" => [
#"snv=/path/to/CADD_whole_genome_SNVs.tsv.gz",
#"indels=/path/to/CADD_GRCh38_1.6_InDels.tsv.gz",
#"snv_pig=/path/to/ALL_pCADD-PHRED-scores.tsv.gz",
#"sv=/path/to/CADD_prescored_variants.tsv.gz"
]
},
# CAPICE
# https://github.com/ensembl-variation/VEP_plugins/blob/main/CAPICE.pm
# Requires tabix-indexed data files as params (one for InDels, another for SNVs)
# No other parameters so no form required
# data file currently only available for GRCh37
{
"key" => "CAPICE",
"label" => "CAPICE",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations (CAPICE) is a tool for scoring the pathogenicity of single nucleotide variants and insertion/deletion variants in the human genome. CAPICE uses a gradient boosting tree model trained with multiple genomic annotations used by CADD score and based on clinical significance.",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/112/CAPICE.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"/path/to/capice_v1.0_build37_indels.tsv.gz",
#"/path/to/capice_v1.0_build37_snvs.tsv.gz"
]
},
# FATHMM
{
"key" => "FATHMM",
"label" => "FATHMM",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/112/FATHMM.pm"
},
# FATHMM-MKL
# https://github.com/ensembl-variation/VEP_plugins/blob/main/FATHMM_MKL.pm
# Requires tabix-indexed data file as first param
# No other parameters so no form required
# data file currently only available for GRCh37
{
"key" => "FATHMM_MKL",
"label" => "FATHMM-MKL",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "FATHMM-MKL predicts functional consequences of variants, both coding and non-coding.",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/112/FATHMM_MKL.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"/path/to/fathmm-MKL_Current.tab.gz"
]
},
# GWAVA
# https://www.sanger.ac.uk/sanger/StatGen_Gwava
# Requires tabix-indexed BED data file from ftp://ftp.sanger.ac.uk/pub/resources/software/gwava/v1.0/VEP_plugin/
# data file currently only available for GRCh37
{
"key" => "Gwava",
"label" => "GWAVA",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "Retrieves precomputed Genome Wide Annotation of VAriants (GWAVA) scores for any variant that overlaps a known variant from the Ensembl variation database",
"plugin_url" => "ftp://ftp.sanger.ac.uk/pub/resources/software/gwava/v1.0/VEP_plugin/Gwava.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
"@*",
# "/path/to/gwava_scores.bed.gz"
],
"form" => [
{
"name" => "model",
"label" => "Model",
"type" => "dropdown",
"values" => [
{ "value" => "region", "caption" => "Region" },
{ "value" => "tss", "caption" => "TSS" },
{ "value" => "unmatched", "caption" => "Unmatched" }
],
"value" => "region",
},
],
},
# Carol
# https://github.com/ensembl-variation/VEP_plugins/blob/main/Carol.pm
# Requires Math/CDF Perl module
{
"key" => "Carol",
"helptip" => "Calculates the Combined Annotation scoRing toOL (CAROL) score for a missense mutation based on the pre-calculated SIFT and PolyPhen scores",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/112/Carol.pm",
"requires_install" => 1,
"species" => [
"homo_sapiens"
],
},
# Condel
# https://github.com/ensembl-variation/VEP_plugins/blob/main/Condel.pm
# Requires path to config directory as first param
# config directory is checked out as part of VEP_plugins repo, as /[path]/VEP_plugins/config/Condel/config
# Within that dir, edit condel_SP.conf so that condel.dir points to /[path]/VEP_plugins/config/Condel
{
"key" => "Condel",
"helptip" => "Calculates the Consensus Deleteriousness (Condel) score for a missense mutation based on the pre-calculated SIFT and PolyPhen scores",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/112/Condel.pm",
"requires_install" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/config/Condel/config",
"@*"
],
"form" => [
{
"name" => "score_pred",
"label" => "Score/prediction",
"type" => "dropdown",
"values" => [
{ "value" => "b", "caption" => "Prediction and score" },
{ "value" => "p", "caption" => "Prediction only" },
{ "value" => "s", "caption" => "Score only" }
],
"value" => "b",
},
],
},
# LOFTEE
# See https://github.com/konradjk/loftee for details
{
"key" => "LoF",
"helptip" => "LOFTEE identifies 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)
{
"key" => "LoFtool",
"helptip" => "Provides a per-gene rank of genic intolerance and consequent susceptibility to disease based on the ratio of Loss-of-function (LoF) to synonymous mutations in ExAC data",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/112/LoFtool.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/LoFtool_scores.txt"
]
},
# MPC
# Requires fordist_constraint_official_mpc_values.txt.gz data file
{
"key" => "MPC",
"helptip" => "MPC is a missense deleteriousness metric based on the analysis of genic regions depleted of missense mutations in ExAC",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/112/MPC.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/fordist_constraint_official_mpc_values.txt.gz"
]
},
# MTR
# Requires mtrflatfile_1.0.txt.gz data file from ftp://mtr-viewer.mdhs.unimelb.edu.au/pub
{
"key" => "MTR",
"helptip" => "MTR scores quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence",