conf.toml

# File used by VCFanno to define how a VCF file should be annotated

[[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/cadd_v1.3.vcf.gz"
names=["CADD_Phred", "CADD_Raw"]
ops=["self", "self"]
fields=["phred", "raw"]
# Used process outlined on https://github.com/brentp/vcfanno/blob/master/docs/examples/cadd.md to create CADD vcf file from original download

[[annotation]]
file="annotations/reheadered.MGRB.vcf.gz"
fields=["AC", "AF"]
ops=["self", "self"]
names=["MGRB_AC", "MGRB_AF"]

[[annotation]]
file="annotations/dbscSNV1.1.vcf.gz"
fields = ["ada_score", "rf_score"]
ops=["self", "self"]
names=["dbscSNV_AdaBoost_Score", "dbscSNV_RandomForest_Score"]

[[annotation]]
file="annotations/hg19_spidex.sorted.vcf.gz"
fields = ["dpsi_max_tissue", "dpsi_zscore"]
ops=["self", "self"]
names=["SPIDEX_dPSI_Max_Tissue", "SPIDEX_dPSI_Zscore"]

[[annotation]]
file="annotations/gencode_v26_branchpoints.csv.liftedtohg19.sorted.vcf.gz"
fields = ["branchpoint_prob", "U2_binding_energy"]
ops=["self", "self"]
names=["Branchpointer_Branchpoint_Prob", "Branchpointer_U2_Binding_Energy"]

[[annotation]]
file="subsetting/gencode.v28lift37.annotation.gtf.bed.gz"
columns = [4, 5]
ops=["self", "self"]
names=["Gene_Symbol", "Gene_Strand"]