rule_columns.md

Rule columns

Minimal recommended features:

sample.id, SYMBOL, HGVSp, HGVSc, Consequence, IMPACT, genotype, gnomAD_AF, AC, AF, (AF.x, AF.y)*, AN, start, end, width, strand, Allele, Gene, Feature_type, Feature, BIOTYPE, EXON, INTRON, cDNA_position, CDS_position, Protein_position, Amino_acids, Codons, CANONICAL,

Secondary recommended features:

ACMG_count, ACMG_highest, ACMG_total_score, comp_het_flag, Inheritance, CLIN_SIG, seqnames, Existing_variation, DISTANCE, STRAND, FLAGS, VARIANT_CLASS, SYMBOL_SOURCE, HGNC_ID, CCDS, ENSP, SWISSPROT, TREMBL, HGVS_OFFSET, CADD_PHRED

QC recommended features:

BaseQRankSum, DB, DP, DS, END, ExcessHet, FS, InbreedingCoeff, MLEAC, MLEAF, MQ, MQRankSum, QD, RAW_MQ, ReadPosRankSum, SOR, OLD_MULTIALLELIC,

Where these are used

Apply ACMG PM2 Criterion

gnomAD_AF gnomad_max

Apply ACMG PM3 Criterion

ACMG_PS1 ACMG_PS5 ACMG_PM3 ACMG_PP3 CADD_PHRED comp_het_flag MetaLR_pred MutationAssessor_pred PolyPhen REVEL_rankscore sample SIFT SYMBOL

Apply ACMG PS1 Criterion

ACMG_PS1 CLIN_SIG

Apply ACMG PS5 Criterion

ACMG_PS5 comp_het_flag IMPACT sample SYMBOL

Apply ACMG PVS1 Criterion

ACMG_PVS1 comp_het_flag genotype IMPACT Inheritance sample SYMBOL

Apply Varsome In-silico Predictions for ACMG PP3 Criterion

Engine pathogenic_type Moderate_pathogenic_GE Strong_pathogenic_GE Supporting_pathogenic_GE

Renaming logic: Match engine names with df columns

BayesDel_addAF, BayesDel_addAF_score BayesDel_noAF, BayesDel_noAF_score CADD, CADD_PHRED DANN, DANN_score EIGEN, Eigen.raw_coding EIGEN-PC, Eigen.PC.phred_coding FATHMM, FATHMM_score FATHMM-MKL, fathmm.MKL_coding_score FATHMM-XF, fathmm.XF_coding_score LRT, LRT_score M-CAP, M.CAP_score MetaLR, MetaLR_score MetaSVM, MetaSVM_score MetaRNN, MetaRNN_score MutPred, MutPred_score MutationAssessor, MutationAssessor_score MutationTaster, MutationTaster_score phastCons100way_vertebrate, phastCons100way_vertebrate Polyphen2-HDIV, Polyphen2_HDIV_score Polyphen2-HVAR, Polyphen2_HVAR_score PROVEAN, PROVEAN_score REVEL, REVEL_score SIFT, SIFT_score