From feeb2ef2d6aac502e493939927d925bab401cec1 Mon Sep 17 00:00:00 2001 From: Nuno Agostinho Date: Tue, 27 Aug 2024 16:07:21 +0100 Subject: [PATCH] Document VEP plugin Paralogues --- root/documentation/vep.conf | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/root/documentation/vep.conf b/root/documentation/vep.conf index 12b146d2..afc5e111 100644 --- a/root/documentation/vep.conf +++ b/root/documentation/vep.conf @@ -243,6 +243,12 @@ description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by MaveDB database. (plugin details) default=0 + + type=String + description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:
ArgumentDescriptionDefault
clinsigClinical significance term to filter variants; use clnsig=ignore to fetch all paralogue variants, regardless of clinical significanceclnsig=pathogenic
clnsig_match Type of match when filtering variants based on clinical significance: partial, exact or regexclnsig_match=partial
fieldsColon-separated list of information from paralogue variants to output; use fields=all to print all fieldsfields=identifier:alleles:clinical_significance
min_perc_covMinimum alignment percentage of the peptide associated with the input variantmin_perc_cov=0
min_perc_posMinimum percentage of positivity (similarity) between both homologuesmin_perc_pos=50
(plugin details) + default=Not used + example=clnsig=pathogenic,clnsig_match=exact,fields=all + type=Boolean description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (plugin details) @@ -592,6 +598,12 @@ description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by MaveDB database. (plugin details) default=0 + + type=String + description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:
ArgumentDescriptionDefault
clinsigClinical significance term to filter variants; use clnsig=ignore to fetch all paralogue variants, regardless of clinical significanceclnsig=pathogenic
clnsig_match Type of match when filtering variants based on clinical significance: partial, exact or regexclnsig_match=partial
fieldsColon-separated list of information from paralogue variants to output; use fields=all to print all fieldsfields=identifier:alleles:clinical_significance
min_perc_covMinimum alignment percentage of the peptide associated with the input variantmin_perc_cov=0
min_perc_posMinimum percentage of positivity (similarity) between both homologuesmin_perc_pos=50
(plugin details) + default=Not used + example=clnsig=pathogenic,clnsig_match=exact,fields=all + type=Boolean description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (plugin details) @@ -929,6 +941,12 @@ description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by MaveDB database. (plugin details) default=0 + + type=String + description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:
ArgumentDescriptionDefault
clinsigClinical significance term to filter variants; use clnsig=ignore to fetch all paralogue variants, regardless of clinical significanceclnsig=pathogenic
clnsig_match Type of match when filtering variants based on clinical significance: partial, exact or regexclnsig_match=partial
fieldsColon-separated list of information from paralogue variants to output; use fields=all to print all fieldsfields=identifier:alleles:clinical_significance
min_perc_covMinimum alignment percentage of the peptide associated with the input variantmin_perc_cov=0
min_perc_posMinimum percentage of positivity (similarity) between both homologuesmin_perc_pos=50
(plugin details) + default=Not used + example=clnsig=pathogenic,clnsig_match=exact,fields=all + type=Boolean description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (plugin details) @@ -1260,6 +1278,12 @@ description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by MaveDB database. (plugin details) default=0 + + type=String + description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:
ArgumentDescriptionDefault
clinsigClinical significance term to filter variants; use clnsig=ignore to fetch all paralogue variants, regardless of clinical significanceclnsig=pathogenic
clnsig_match Type of match when filtering variants based on clinical significance: partial, exact or regexclnsig_match=partial
fieldsColon-separated list of information from paralogue variants to output; use fields=all to print all fieldsfields=identifier:alleles:clinical_significance
min_perc_covMinimum alignment percentage of the peptide associated with the input variantmin_perc_cov=0
min_perc_posMinimum percentage of positivity (similarity) between both homologuesmin_perc_pos=50
(plugin details) + default=Not used + example=clnsig=pathogenic,clnsig_match=exact,fields=all + type=Boolean description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (plugin details) @@ -1602,6 +1626,12 @@ description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by MaveDB database. (plugin details) default=0 + + type=String + description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:
ArgumentDescriptionDefault
clinsigClinical significance term to filter variants; use clnsig=ignore to fetch all paralogue variants, regardless of clinical significanceclnsig=pathogenic
clnsig_match Type of match when filtering variants based on clinical significance: partial, exact or regexclnsig_match=partial
fieldsColon-separated list of information from paralogue variants to output; use fields=all to print all fieldsfields=identifier:alleles:clinical_significance
min_perc_covMinimum alignment percentage of the peptide associated with the input variantmin_perc_cov=0
min_perc_posMinimum percentage of positivity (similarity) between both homologuesmin_perc_pos=50
(plugin details) + default=Not used + example=clnsig=pathogenic,clnsig_match=exact,fields=all + type=Boolean description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (plugin details) @@ -1952,6 +1982,12 @@ description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by MaveDB database. (plugin details) default=0 + + type=String + description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:
ArgumentDescriptionDefault
clinsigClinical significance term to filter variants; use clnsig=ignore to fetch all paralogue variants, regardless of clinical significanceclnsig=pathogenic
clnsig_match Type of match when filtering variants based on clinical significance: partial, exact or regexclnsig_match=partial
fieldsColon-separated list of information from paralogue variants to output; use fields=all to print all fieldsfields=identifier:alleles:clinical_significance
min_perc_covMinimum alignment percentage of the peptide associated with the input variantmin_perc_cov=0
min_perc_posMinimum percentage of positivity (similarity) between both homologuesmin_perc_pos=50
(plugin details) + default=Not used + example=clnsig=pathogenic,clnsig_match=exact,fields=all + type=Boolean description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (plugin details)