Comment annotation files

CCICB · Apr 3, 2023 · e0d07b5 · e0d07b5
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Showing 3 changed files with 24 additions and 21 deletions.
diff --git a/annotations/conf_introme.toml b/annotations/conf_introme.toml
@@ -1,31 +1,36 @@
 # File used by VCFanno to define how a VCF file should be annotated
 
+# MMSplice (computed during Introme)
 [[annotation]]
-file="introme_annotate.mmsplice.vcf.gz"
+file = "introme_annotate.mmsplice.vcf.gz"
 fields = ["alt_acceptor", "alt_acceptor_intron", "alt_donor", "alt_donor_intron", "alt_exon", "delta_logit_PSI", "pathogenicity", "ref_acceptor", "ref_acceptor_intron", "ref_donor", "ref_donor_intron", "ref_exon"]
-ops=["self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self"]
-names=["MMSplice_alt_acceptor", "MMSplice_alt_acceptor_intron", "MMSplice_alt_donor", "MMSplice_alt_donor_intron", "MMSplice_alt_exon", "MMSplice_delta_logit_PSI", "MMSplice_pathogenicity", "MMSplice_ref_acceptor", "MMSplice_ref_acceptor_intron", "MMSplice_ref_donor", "MMSplice_ref_donor_intron", "MMSplice_ref_exon"]
+ops = ["self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self"]
+names = ["MMSplice_alt_acceptor", "MMSplice_alt_acceptor_intron", "MMSplice_alt_donor", "MMSplice_alt_donor_intron", "MMSplice_alt_exon", "MMSplice_delta_logit_PSI", "MMSplice_pathogenicity", "MMSplice_ref_acceptor", "MMSplice_ref_acceptor_intron", "MMSplice_ref_donor", "MMSplice_ref_donor_intron", "MMSplice_ref_exon"]
 
+# Introme AG/GT Computation (computed during Introme)
 [[annotation]]
-file="introme_annotate.functions.vcf.gz"
-fields = ["variant_type", "ag_created", "ag_lost", 'gt_created', 'gt_lost']
-ops=["self","self","self", "self", "self"]
-names=["Variant_Type", "AG_Created", "AG_Lost", "GT_Created", "GT_Lost"]
+file = "introme_annotate.functions.vcf.gz"
+fields = ["variant_type", "ag_created", "ag_lost", "gt_created", "gt_lost"]
+ops = ["uniq","uniq","uniq", "uniq", "uniq"]
+names = ["Variant_Type", "AG_Created", "AG_Lost", "GT_Created", "GT_Lost"]
 
+# Spliceogen (computed during Introme)
 [[annotation]]
 file = "introme_annotate.spliceogen.vcf.gz"
 fields = ["mesDonRef", "mesDonAlt", "mesAccRef", "mesAccAlt", "ESEmaxRef", "ESEmaxAlt", "ESEminRef", "ESEminAlt", "DonGainP", "AccGainP", "DonLossP", "AccLossP"]
 ops = ["self", "self","self" ,"self", "self", "self", "self", "self", "self", "self", "self", "self"]
 names = ["mesDonRef", "mesDonAlt", "mesAccRef", "mesAccAlt", "ESEmaxRef", "ESEmaxAlt", "ESEminRef", "ESEminAlt", "DonGainP", "AccGainP", "DonLossP", "AccLossP"]
 
+# ESE Scoring (computed during Introme)
 [[annotation]]
 file = "introme_annotate.ESE.vcf.gz"
 fields = ["SRSF1_ref", "SRSF1_alt", "SRSF1_igM_ref", "SRSF1_igM_alt", "SRSF2_ref", "SRSF2_alt", "SRSF5_ref", "SRSF5_alt", "SRSF6_ref", "SRSF6_alt", "hnRNPA1_ref", "hnRNPA1_alt"]
 ops = ["max", "max", "max", "max", "max", "max", "max", "max", "max", "max", "max", "max"]
 names = ["SRSF1_ref", "SRSF1_alt", "SRSF1_igM_ref", "SRSF1_igM_alt", "SRSF2_ref", "SRSF2_alt", "SRSF5_ref", "SRSF5_alt", "SRSF6_ref", "SRSF6_alt", "hnRNPA1_ref", "hnRNPA1_alt"]
 
+# SpliceAI (computed during Introme)
 [[annotation]]
 file = "introme_annotate.spliceai.vcf.gz"
 fields = ["DS_AG", "DS_AL", "DS_DG", "DS_DL", "DP_AG", "DP_AL", "DP_DG", "DP_DL"]
-ops = ["self", "self","self" ,"self", "self", "self", "self", "self"]
+ops = ["max", "max","max" ,"max", "self", "self", "self", "self"]
 names = ["SpliceAI_Acceptor_Gain", "SpliceAI_Acceptor_Loss", "SpliceAI_Donor_Gain", "SpliceAI_Donor_Loss", "DP_AG", "DP_AL", "DP_DG", "DP_DL"]
diff --git a/annotations/gencode.hg19.toml b/annotations/gencode.hg19.toml
@@ -1,5 +1,4 @@
 ## Gencode annotations
-## Update file path
 [[annotation]]
 file = "annotations/gencode.v42lift37.basic.annotation.rmchr.gtf.gz"
 columns = [3,7,9]
@@ -28,9 +27,8 @@ type = "String"
 fields = ["gencode_types","gencode"]
 op = "delete"
 
-# Optional Allele frequency annotations using gnomAD
-# [[annotation]]
-# file="annotations/gnomad.genomes.sites.merged.AF_AC_AN_only.vcf.gz"
-# fields = ["AF", "AC", "AN", "POPMAX", "AF_POPMAX", "AC_POPMAX", "AN_POPMAX"]
-# ops=["self", "self", "self", "self", "self", "self", "self"]
-# names=["gnomAD_AF", "gnomAD_AC", "gnomAD_AN", "gnomAD_PopMax", "gnomAD_PM_AF", "gnomAD_PM_AC", "gnomAD_PM_AN"]
+[[annotation]]
+file="annotations/gnomad.genomes.sites.merged.AF_AC_AN_only.vcf.gz"
+fields = ["AF", "AC", "AN", "POPMAX", "AF_POPMAX", "AC_POPMAX", "AN_POPMAX"]
+ops=["self", "self", "self", "self", "self", "self", "self"]
+names=["gnomAD_AF", "gnomAD_AC", "gnomAD_AN", "gnomAD_PopMax", "gnomAD_PM_AF", "gnomAD_PM_AC", "gnomAD_PM_AN"]
diff --git a/annotations/gencode.hg38.toml b/annotations/gencode.hg38.toml
@@ -1,6 +1,6 @@
 ## Gencode annotations
 [[annotation]]
-file = "annotations/gencode.v41.annotation.gtf.gz"
+file = "annotations/gencode.v43.annotation.gtf.gz"
 columns = [3,7,9]
 ops = ["self","uniq","self"]
 names = ["gencode_types","strand","gencode"]
@@ -28,8 +28,8 @@ fields = ["gencode_types","gencode"]
 op = "delete"
 
 # Optional Allele frequency annotations using gnomAD
-# [[annotation]]
-# file="annotations/gnomad.genomes.sites.merged.AF_AC_AN_only.vcf.gz"
-# fields = ["AF", "AC", "AN", "POPMAX", "AF_POPMAX", "AC_POPMAX", "AN_POPMAX"]
-# ops=["self", "self", "self", "self", "self", "self", "self"]
-# names=["gnomAD_AF", "gnomAD_AC", "gnomAD_AN", "gnomAD_PopMax", "gnomAD_PM_AF", "gnomAD_PM_AC", "gnomAD_PM_AN"]
+[[annotation]]
+file="annotations/gnomad.zero.hg38.vcf.gz"
+fields = ["AF", "AC", "AN", "POPMAX", "AF_POPMAX", "AC_POPMAX", "AN_POPMAX"]
+ops=["self", "self", "self", "self", "self", "self", "self"]
+names=["gnomAD_AF", "gnomAD_AC", "gnomAD_AN", "gnomAD_PopMax", "gnomAD_PM_AF", "gnomAD_PM_AC", "gnomAD_PM_AN"]