From 20c1b907642adaf041ea485c60b3ab1c1e8a2c0e Mon Sep 17 00:00:00 2001 From: gorgitko Date: Mon, 23 Mar 2026 22:20:02 +0100 Subject: [PATCH 1/2] use new column name for gnomAD OTH AF --- R/sarek_vcf.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/sarek_vcf.R b/R/sarek_vcf.R index caa02f9..e81dfb8 100644 --- a/R/sarek_vcf.R +++ b/R/sarek_vcf.R @@ -319,7 +319,7 @@ convert_vcf_df_to_finalist <- function(vcf_df) { `gnomAD ASJ AF` = dplyr::any_of(c("gnom_ad_asj_af", "gnom_a_de_asj_af")), `gnomAD EAS AF` = dplyr::any_of(c("gnom_ad_eas_af", "gnom_a_de_eas_af")), `gnomAD FIN AF` = dplyr::any_of(c("gnom_ad_fin_af", "gnom_a_de_fin_af")), - `gnomAD OTH AF` = dplyr::any_of(c("gnom_ad_oth_af", "gnom_a_de_oth_af")), + `gnomAD OTH AF` = dplyr::any_of(c("gnom_ad_oth_af", "gnom_a_de_oth_af", "gnom_a_de_remaining_af")), `gnomAD SAS AF` = dplyr::any_of(c("gnom_ad_sas_af", "gnom_a_de_sas_af")), `Ensembl transcript ID` = feature, `Pubmed ID` = pubmed, From 1ba3e0f7ec89163276526db5a69de9b8590c97e7 Mon Sep 17 00:00:00 2001 From: gorgitko Date: Tue, 31 Mar 2026 22:49:36 +0200 Subject: [PATCH 2/2] update conversion to finalistDX excel: - round some numeric columns to two digits - Calculate "Variant occurred" based on CHROM+POS - Add new "Variant occurred (with REF+ALT)" based on CHROM+POS+REF+ALT - Rename some dangling columns - Remove trailing zeros when converting numeric columns to comma separated decimal point character --- R/sarek_vcf.R | 69 +- .../2021_09_MR-Mikro4_deepvariant.csv | 3218 +-- .../2021_09_MR-Mikro4_haplotypecaller.csv | 4680 ++--- .../sarek_vcf/2021_09_MR-Mikro4_strelka.csv | 3404 ++-- ...2024_05_24_Panel_run_2_haplotypecaller.csv | 4908 ++--- ...03_Panel_run_23_BRCA_255_tkane_mutect2.csv | 5736 +++--- ...6_validace1_Hluchota50_haplotypecaller.csv | 16186 ++++++++-------- ...aplotypecaller.filtered_VEP.ann.vcf.gz.rds | Bin 93342 -> 92804 bytes ...aplotypecaller.filtered_VEP.ann.vcf.gz.rds | Bin 87258 -> 86950 bytes ...aplotypecaller.filtered_VEP.ann.vcf.gz.rds | Bin 93507 -> 93313 bytes ...aplotypecaller.filtered_VEP.ann.vcf.gz.rds | Bin 92316 -> 91794 bytes ...A255tk.mutect2.filtered_VEP.ann.vcf.gz.rds | Bin 125745 -> 124239 bytes ...A255tk.mutect2.filtered_VEP.ann.vcf.gz.rds | Bin 112226 -> 111231 bytes ...aplotypecaller.filtered_VEP.ann.vcf.gz.rds | Bin 259677 -> 261365 bytes ...aplotypecaller.filtered_VEP.ann.vcf.gz.rds | Bin 244235 -> 244969 bytes ...aplotypecaller.filtered_VEP.ann.vcf.gz.rds | Bin 251794 -> 252693 bytes tests/testthat/test-sarek_vcf.R | 9 +- 17 files changed, 19123 insertions(+), 19087 deletions(-) diff --git a/R/sarek_vcf.R b/R/sarek_vcf.R index e81dfb8..cc6d948 100644 --- a/R/sarek_vcf.R +++ b/R/sarek_vcf.R @@ -1,3 +1,9 @@ +.COLUMNS_TO_ROUND <- c( + "Variant Frequency", + "Variant occurred [%]", + "Variant occurred (with REF+ALT) [%]" +) + .validate_vcf_files <- function(vcf_files) { vcf_files_missing <- vcf_files[!fs::file_exists(vcf_files)] if (!rlang::is_empty(vcf_files_missing)) { @@ -235,27 +241,26 @@ calculate_variant_stats <- function(vcf_df, vc_tool = SUPPORTED_VC_TOOLS) { convert_vcf_df_to_finalist <- function(vcf_df) { n_samples <- unique(vcf_df$SAMPLE) %>% length() - ## count variant occurrences within all samples - n_ids <- vcf_df %>% - ## distinct IDs within each sample as there are multiple annotations per a single ID - dplyr::distinct(SAMPLE, CHROM, POS, ID, REF, ALT) %>% - dplyr::group_by(CHROM, POS, ID, REF, ALT) %>% - dplyr::tally() %>% - dplyr::mutate( - `Variant occurred` = glue("{n}/{n_samples}") %>% as.character(), - `Variant occurred [%]` = scales::percent(n / n_samples, suffix = "", accuracy = 0.01) - ) + variant_occurred_simple <- .calculate_variant_occurred( + vcf_df, + group_by = c("CHROM", "POS"), + output_column = "Variant occurred" + ) + variant_occurred_ref_alt <- .calculate_variant_occurred( + vcf_df, + group_by = c("CHROM", "POS", "REF", "ALT"), + output_column = "Variant occurred (with REF+ALT)" + ) vcf_df <- vcf_df %>% - dplyr::left_join(n_ids, by = c("CHROM", "POS", "ID", "REF", "ALT")) %>% + dplyr::left_join(variant_occurred_simple, by = c("CHROM", "POS")) %>% + dplyr::left_join(variant_occurred_ref_alt, by = c("CHROM", "POS", "REF", "ALT")) %>% tidyr::extract(sift, c("sift_class", "sift_score"), regex = "^(.+)\\((.*)\\)$", remove = FALSE, convert = TRUE) %>% tidyr::extract(poly_phen, c("poly_phen_class", "poly_phen_score"), regex = "^(.+)\\((.*)\\)$", remove = FALSE, convert = TRUE) %>% dplyr::mutate( Genotype = .parse_genotype(gt_GT), Canonical = dplyr::if_else(canonical == "YES", "YES", "NO"), `ClinVar Allele ID` = NA_character_, - `ClinVar disease name` = NA_character_, - `ClinVar review status` = NA_character_, `LRT pred` = NA_real_, `CADD phred` = NA_real_, `DANN score` = NA_real_, @@ -324,8 +329,6 @@ convert_vcf_df_to_finalist <- function(vcf_df) { `Ensembl transcript ID` = feature, `Pubmed ID` = pubmed, SAMPLE_variant_key, - `ClinVar disease name`, - `ClinVar review status`, `LRT pred`, `CADD phred`, `DANN score`, @@ -339,8 +342,11 @@ convert_vcf_df_to_finalist <- function(vcf_df) { `Depth of alternate reverse`, `ClinVar ID` = dplyr::any_of("clinvar_id"), `ClinVar HGVS` = dplyr::any_of("clinvar_hgvs"), - `ClinVar Review` = dplyr::any_of("clinvar_review"), - dplyr::any_of(c("clin_sig", "clinvar_clnsig")) + `ClinVar disease name` = dplyr::any_of("clinvar_trait"), + `ClinVar review status` = dplyr::any_of("clinvar_review"), + dplyr::any_of(c("clin_sig", "clinvar_clnsig")), + `Variant occurred (with REF+ALT)`, + `Variant occurred (with REF+ALT) [%]` ) if ("clinvar_clnsig" %in% colnames(vcf_df)) { @@ -349,7 +355,7 @@ convert_vcf_df_to_finalist <- function(vcf_df) { `Clinical significance` = dplyr::any_of("clinvar_clnsig"), `Clinical significance (old)` = clin_sig ) %>% - dplyr::relocate(`Clinical significance (old)`, .after = `ClinVar Review`) + dplyr::relocate(`Clinical significance (old)`, .after = `ClinVar review status`) } else { vcf_df <- vcf_df %>% dplyr::rename( @@ -370,7 +376,8 @@ convert_vcf_df_to_finalist <- function(vcf_df) { ), dplyr::across( c( - `Variant occurred [%]`, `Variant Frequency`, `SIFT score`, `PolyPhen score`, `gnomAD AF`, + `Variant occurred [%]`, `Variant occurred (with REF+ALT) [%]`, `Variant Frequency`, + `SIFT score`, `PolyPhen score`, `gnomAD AF`, `gnomAD NFE AF`, `MAX AF`, `gnomAD AF_`, `gnomAD AFR AF`, `gnomAD AMR AF`, `gnomAD ASJ AF`, `gnomAD EAS AF`, `gnomAD FIN AF`, `gnomAD OTH AF`, `gnomAD SAS AF` ), @@ -384,6 +391,7 @@ convert_vcf_df_to_finalist <- function(vcf_df) { ) ) %>% dplyr::mutate(`Variant Frequency` = `Variant Frequency` * 100) %>% + dplyr::mutate(dplyr::across(dplyr::all_of(.COLUMNS_TO_ROUND), ~ round(.x, digits = 2))) %>% dplyr::mutate(dplyr::across(dplyr::where(is.double), .format_float)) %>% dplyr::mutate(dplyr::across(dplyr::everything(), ~tidyr::replace_na(as.character(.), "-"))) %>% dplyr::mutate(dplyr::across(dplyr::everything(), ~dplyr::if_else(. == "", "-", .))) %>% @@ -410,13 +418,34 @@ convert_vcf_df_to_finalist <- function(vcf_df) { } .format_float <- function(values, sep = ",") { - formatted <- formatC(values, format = "f", digits = 6, flag = "", drop0trailing = FALSE) %>% + formatted <- formatC(values, format = "f", digits = 6, flag = "", drop0trailing = TRUE) %>% stringr::str_trim() dplyr::if_else(formatted == "NA", NA_character_, formatted) %>% stringr::str_replace("\\.", ",") } +#' @title Count variant occurrences within all samples +.calculate_variant_occurred <- function(vcf_df, group_by, output_column) { + group_vars <- rlang::syms(group_by) + + col_pct <- glue("{output_column} [%]") + + n_samples <- vcf_df %>% + dplyr::distinct(SAMPLE) %>% + nrow() + + vcf_df %>% + dplyr::distinct(SAMPLE, !!!group_vars) %>% + dplyr::group_by(!!!group_vars) %>% + dplyr::tally() %>% + dplyr::mutate( + !!output_column := glue::glue("{n}/{n_samples}") %>% as.character(), + !!col_pct := scales::percent(n / n_samples, suffix = "", accuracy = 0.01) + ) %>% + dplyr::select(-n) +} + #' @export get_per_sample_variant_stats <- function(vcf_df) { vcf_df %>% diff --git a/tests/testthat/_snaps/sarek_vcf/2021_09_MR-Mikro4_deepvariant.csv b/tests/testthat/_snaps/sarek_vcf/2021_09_MR-Mikro4_deepvariant.csv index a9c250e..d43b84b 100644 --- a/tests/testthat/_snaps/sarek_vcf/2021_09_MR-Mikro4_deepvariant.csv +++ b/tests/testthat/_snaps/sarek_vcf/2021_09_MR-Mikro4_deepvariant.csv @@ -1,1609 +1,1609 @@ -"Name","Variant occurred","Variant occurred [%]","Read Depth","Variant Frequency","Symbol","Chr","Genotype","Variant_class","Coordinate","Feature","MANE Select","MANE Plus Clinical","Canonical","Exon","Intron","HGVSc","HGVSp","VEP dbSNP ID","dbSNP ID","ClinVar Allele ID","Impact","Consequence","Clinical significance","SIFT","SIFT score","PolyPhen","PolyPhen score","gnomAD AF","gnomAD NFE AF","MAX AF","MAX AF POPS","cDNA position","CDS position","Protein position","Amino acids","Codons","Distance","Strand","Somatic","Pheno","Reference","Alternate","Reference depth","Alternate depth","gnomAD AF_","gnomAD AFR AF","gnomAD AMR AF","gnomAD ASJ AF","gnomAD EAS AF","gnomAD FIN AF","gnomAD OTH AF","gnomAD SAS AF","Ensembl transcript ID","Pubmed ID","SAMPLE_variant_key","ClinVar disease name","ClinVar review status","LRT pred","CADD phred","DANN score","FATHMM pred","HGVS offset","codonpos","refcodon","Depth of reference forward","Depth of reference reverse","Depth of alternate forward","Depth of alternate reverse" 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-"MRMIKRO4_2024-21","2/2","100,000000","237","99,578100","AMPD2","chr1","HOM","SNV","109626266","ENST00000528667","NM_001368809.2","-","YES","-","5/18","-","-","-","-","-","MODIFIER","intron_variant","-","-","-","-","-","0,727000","0,640100","0,980700","gnomAD_EAS","-","-","-","-","-","-","1","-","-","C","G","1","236","0,727000","0,756800","0,783200","0,668400","0,980700","0,699300","0,715600","0,857200","ENST00000528667","-","MRMIKRO4_2024-21_chr1_109626266_C_G","-","-","-","-","-","-","-","-","-","-","-","-","-" 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-"MRMIKRO4_2024-21","2/2","100,000000","148","100,000000","-","chr1","HOM","SNV","109627335","ENST00000369843","-","-","YES","-","-","-","-","-","-","-","MODIFIER","downstream_gene_variant","benign","-","-","-","-","0,745800","0,653600","0,981200","EAS","-","-","-","-","-","1082","-1","-","1","A","G","0","148","0,745800","0,874800","0,792400","0,696600","0,980000","0,722100","0,729000","0,859000","ENST00000369843","29047346","MRMIKRO4_2024-21_chr1_109627335_A_G","-","-","-","-","-","-","-","-","-","-","-","-","-" 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-"MRMIKRO4_2024-21","2/2","100,000000","220","100,000000","-","chr1","HOM","SNV","109628274","ENST00000369843","-","-","YES","-","-","-","-","-","-","-","MODIFIER","downstream_gene_variant","benign","-","-","-","-","0,736500","0,653400","0,980600","gnomAD_EAS","-","-","-","-","-","143","-1","0&1","1&1","T","C","0","220","0,736500","0,760500","0,787600","0,690900","0,980600","0,716600","0,724200","0,858800","ENST00000369843","-","MRMIKRO4_2024-21_chr1_109628274_T_C","-","-","-","-","-","-","-","-","-","-","-","-","-" -"MRMIKRO4_2024-21","2/2","100,000000","220","100,000000","AMPD2","chr1","HOM","SNV","109628274","ENST00000528667","NM_001368809.2","-","YES","11/19","-","-","-","-","-","-","LOW","synonymous_variant","benign","-","-","-","-","0,736500","0,653400","0,980600","gnomAD_EAS","1976/4081","1272/2478","424/825","H","caT/caC","-","1","0&1","1&1","T","C","0","220","0,736500","0,760500","0,787600","0,690900","0,980600","0,716600","0,724200","0,858800","ENST00000528667","-","MRMIKRO4_2024-21_chr1_109628274_T_C","-","-","-","-","-","-","-","-","-","-","-","-","-" -"MRMIKRO4_2024-21","1/2","50,000000","234","47,863200","PHGDH","chr1","HET","SNV","119726926","ENST00000641023","NM_006623.4","-","YES","-","4/11","-","-","-","-","-","MODIFIER","intron_variant","-","-","-","-","-","0,019300","0,026400","0,037100","gnomAD_ASJ","-","-","-","-","-","-","1","-","-","G","A","121","112","0,019300","0,004552","0,013500","0,037100","0,000163","0,026280","0,022160","0,007415","ENST00000641023","-","MRMIKRO4_2024-21_chr1_119726926_G_A","-","-","-","-","-","-","-","-","-","-","-","-","-" -"MRMIKRO4_2024-21","2/2","100,000000","286","98,251700","-","chr1","HOM","SNV","119742923","ENSR00001171088","-","-","NO","-","-","-","-","-","-","-","MODIFIER","regulatory_region_variant","benign","-","-","-","-","0,690800","0,679300","0,804000","gnomAD_SAS","-","-","-","-","-","-","-","0&1","1&1","G","A","0","281","0,690800","0,753800","0,686000","0,795100","0,605200","0,573000","0,699300","0,804000","ENSR00001171088","17701893","MRMIKRO4_2024-21_chr1_119742923_G_A","-","-","-","-","-","-","-","-","-","-","-","-","-" -"MRMIKRO4_2024-21","2/2","100,000000","286","98,251700","PHGDH","chr1","HOM","SNV","119742923","ENST00000641023","NM_006623.4","-","YES","11/12","-","-","-","-","-","-","LOW","synonymous_variant","benign","-","-","-","-","0,690800","0,679300","0,804000","gnomAD_SAS","1415/1866","1326/1602","442/533","T","acG/acA","-","1","0&1","1&1","G","A","0","281","0,690800","0,753800","0,686000","0,795100","0,605200","0,573000","0,699300","0,804000","ENST00000641023","17701893","MRMIKRO4_2024-21_chr1_119742923_G_A","-","-","-","-","-","-","-","-","-","-","-","-","-" -"MRMIKRO4_2024-21","2/2","100,000000","231","99,567100","BNIPL","chr1","HOM","SNV","151034063","ENST00000368931","NM_138278.4","-","YES","-","-","-","-","-","-","-","MODIFIER","upstream_gene_variant","-","-","-","-","-","0,848800","0,861000","0,873200","gnomAD_EAS","-","-","-","-","-","2523","1","-","1","C","A","0","230","0,848800","0,817300","0,868900","0,845400","0,873200","0,828900","0,839300","0,799700","ENST00000368931","30239722&31669095","MRMIKRO4_2024-21_chr1_151034063_C_A","-","-","-","-","-","-","-","-","-","-","-","-","-" 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Depth","Variant Frequency","Symbol","Chr","Genotype","Variant_class","Coordinate","Feature","MANE Select","MANE Plus Clinical","Canonical","Exon","Intron","HGVSc","HGVSp","VEP dbSNP ID","dbSNP ID","ClinVar Allele ID","Impact","Consequence","Clinical significance","SIFT","SIFT score","PolyPhen","PolyPhen score","gnomAD AF","gnomAD NFE AF","MAX AF","MAX AF POPS","cDNA position","CDS position","Protein position","Amino acids","Codons","Distance","Strand","Somatic","Pheno","Reference","Alternate","Reference depth","Alternate depth","gnomAD AF_","gnomAD AFR AF","gnomAD AMR AF","gnomAD ASJ AF","gnomAD EAS AF","gnomAD FIN AF","gnomAD OTH AF","gnomAD SAS AF","Ensembl transcript ID","Pubmed ID","SAMPLE_variant_key","ClinVar disease name","ClinVar review status","LRT pred","CADD phred","DANN score","FATHMM pred","HGVS offset","codonpos","refcodon","Depth of reference forward","Depth of reference reverse","Depth of alternate forward","Depth of alternate reverse" 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Frequency","Symbol","Chr","Genotype","Variant_class","Coordinate","Feature","MANE Select","MANE Plus Clinical","Canonical","Exon","Intron","HGVSc","HGVSp","VEP dbSNP ID","dbSNP ID","ClinVar Allele ID","Impact","Consequence","Clinical significance","SIFT","SIFT score","PolyPhen","PolyPhen score","gnomAD AF","gnomAD NFE AF","MAX AF","MAX AF POPS","cDNA position","CDS position","Protein position","Amino acids","Codons","Distance","Strand","Somatic","Pheno","Reference","Alternate","Reference depth","Alternate depth","gnomAD AF_","gnomAD AFR AF","gnomAD AMR AF","gnomAD ASJ AF","gnomAD EAS AF","gnomAD FIN AF","gnomAD OTH AF","gnomAD SAS AF","Ensembl transcript ID","Pubmed ID","SAMPLE_variant_key","ClinVar disease name","ClinVar review status","LRT pred","CADD phred","DANN score","FATHMM pred","HGVS offset","codonpos","refcodon","Depth of reference forward","Depth of reference reverse","Depth of alternate forward","Depth of alternate reverse" 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occurred [%]","Read Depth","Variant Frequency","Symbol","Chr","Genotype","Variant_class","Coordinate","Feature","MANE Select","MANE Plus Clinical","Canonical","Exon","Intron","HGVSc","HGVSp","VEP dbSNP ID","dbSNP ID","ClinVar Allele ID","Impact","Consequence","Clinical significance","SIFT","SIFT score","PolyPhen","PolyPhen score","gnomAD AF","gnomAD NFE AF","MAX AF","MAX AF POPS","cDNA position","CDS position","Protein position","Amino acids","Codons","Distance","Strand","Somatic","Pheno","Reference","Alternate","Reference depth","Alternate depth","gnomAD AF_","gnomAD AFR AF","gnomAD AMR AF","gnomAD ASJ AF","gnomAD EAS AF","gnomAD FIN AF","gnomAD OTH AF","gnomAD SAS AF","Ensembl transcript ID","Pubmed ID","SAMPLE_variant_key","ClinVar disease name","ClinVar review status","LRT pred","CADD phred","DANN score","FATHMM pred","HGVS offset","codonpos","refcodon","Depth of reference forward","Depth of reference reverse","Depth of alternate forward","Depth of alternate reverse" 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occurred","Variant occurred [%]","Read Depth","Variant Frequency","Symbol","Chr","Genotype","Variant_class","Coordinate","Feature","MANE Select","MANE Plus Clinical","Canonical","Exon","Intron","HGVSc","HGVSp","VEP dbSNP ID","dbSNP ID","ClinVar Allele ID","Impact","Consequence","Clinical significance","SIFT","SIFT score","PolyPhen","PolyPhen score","gnomAD AF","gnomAD NFE AF","MAX AF","MAX AF POPS","cDNA position","CDS position","Protein position","Amino acids","Codons","Distance","Strand","Somatic","Pheno","Reference","Alternate","Reference depth","Alternate depth","gnomAD AF_","gnomAD AFR AF","gnomAD AMR AF","gnomAD ASJ AF","gnomAD EAS AF","gnomAD FIN AF","gnomAD OTH AF","gnomAD SAS AF","Ensembl transcript ID","Pubmed ID","SAMPLE_variant_key","ClinVar disease name","ClinVar review status","LRT pred","CADD phred","DANN score","FATHMM pred","HGVS offset","codonpos","refcodon","Depth of reference forward","Depth of reference reverse","Depth of alternate forward","Depth of alternate reverse","ClinVar ID","ClinVar HGVS","ClinVar Review","Clinical significance (old)" -"4191-25-HLUCHOTA50-F","3/3","100,000000","443","50,338600","CDC14A","chr1","HET","SNV","100352730","NM_003672.4","ENST00000336454.5","-","YES","1/16","-","NM_003672.4:c.-225A>T","-","rs527644","rs527644","-","MODIFIER","5_prime_UTR_variant","-","-","-","-","-","-","-","0,933100","gnomADg_AMI","225/4231","-","-","-","-","-","1","-","1","A","T","220","223","-","-","-","-","-","-","-","-","NM_003672.4","-","4191-25-HLUCHOTA50-F_chr1_100352730_A_T","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","benign" 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+"4191-25-HLUCHOTA50-F","2/3","66,67","83","39,76","PNPT1","chr2","HET","insertion","55673096","NM_033109.5","ENST00000447944.7","-","YES","-","8/27","NM_033109.5:c.680-18_680-17insT","-","rs146633902","rs146633902","-","LOW","splice_polypyrimidine_tract_variant&intron_variant","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-1","-","-","G","GA","50","33","-","-","-","-","-","-","-","-","NM_033109.5","-","4191-25-HLUCHOTA50-F_chr2_55673096_G_GA","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","2/3","66,67" +"4191-25-HLUCHOTA50-F","2/3","66,67","202","100","FANCL","chr2","HOM","SNV","58161561","NM_018062.4","ENST00000233741.9","-","YES","12/14","-","NM_018062.4:c.981T>C","NP_060532.2:p.Ser327=","rs848291","rs848291","-","LOW","synonymous_variant","-","-","-","-","-","0,6434","0,6088","0,947","AFR","993/1658","981/1128","327/375","S","tcT/tcC","-","-1","0&1","1&1","A","G","0","202","0,6434","0,9094","0,6799","0,5516","0,5582","0,6568","0,6232","0,6654","NM_018062.4","-","4191-25-HLUCHOTA50-F_chr2_58161561_A_G","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","benign","2/3","66,67" +"4191-25-HLUCHOTA50-F","2/3","66,67","261","85,44","FANCL","chr2","HET_alt","insertion","58226708","NM_018062.4","ENST00000233741.9","-","YES","-","4/13","NM_018062.4:c.273+19_273+20insT","-","rs372101290","rs372101290","-","MODIFIER","intron_variant","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-1","-","-","G","GA,GAA","38","223","-","-","-","-","-","-","-","-","NM_018062.4","-","4191-25-HLUCHOTA50-F_chr2_58226708_G_GA,GAA","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","1/3","33,33" +"4191-25-HLUCHOTA50-F","3/3","100","81","45,68","ATP6V1B1","chr2","HET","SNV","70935866","NM_001692.4","ENST00000234396.10","-","YES","-","-","-","-","rs11685700","rs11685700","-","MODIFIER","upstream_gene_variant","-","-","-","-","-","-","-","0,6642","gnomADg_FIN","-","-","-","-","-","34","1","-","1","A","G","44","37","-","-","-","-","-","-","-","-","NM_001692.4","-","4191-25-HLUCHOTA50-F_chr2_70935866_A_G","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","benign","3/3","100" +"4191-25-HLUCHOTA50-F","3/3","100","267","50,56","ATP6V1B1","chr2","HET","SNV","70935956","NM_001692.4","ENST00000234396.10","-","YES","1/14","-","NM_001692.4:c.2T>C","NP_001683.2:p.Met1?","rs11681642","rs11681642","-","HIGH","start_lost","Benign","deleterious_low_confidence","0","benign","0,234","0,4001","0,4371","0,5132","gnomADg_AMI","57/1907","2/1542","1/513","M/T","aTg/aCg","-","1","0&1","1&1","T","C","132","135","0,4001","0,3808","0,2608","0,3666","0,3918","0,4947","0,4052","0,3789","NM_001692.4","-","4191-25-HLUCHOTA50-F_chr2_70935956_T_C","-","-","-","-","-","-","-","-","-","-","-","44228","NC_000002.12:g.70935956T>C","not_specified¬_provided&Renal_tubular_acidosis_with_progressive_nerve_deafness","criteria_provided&_multiple_submitters&_no_conflicts","benign","3/3","100" +"4191-25-HLUCHOTA50-F","3/3","100","158","47,47","ATP6V1B1","chr2","HET","SNV","70936095","NM_001692.4","ENST00000234396.10","-","YES","-","1/13","NM_001692.4:c.118+23C>T","-","rs759219","rs759219","-","MODIFIER","intron_variant","-","-","-","-","-","0,3999","0,435","0,5143","gnomADg_AMI","-","-","-","-","-","-","1","0&1","1&1","C","T","83","75","0,3999","0,4065","0,2591","0,3662","0,3843","0,4938","0,4057","0,3786","NM_001692.4","-","4191-25-HLUCHOTA50-F_chr2_70936095_C_T","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","benign","3/3","100" +"4191-25-HLUCHOTA50-F","3/3","100","138","96,38","ALMS1","chr2","HET_alt","sequence_alteration","73385903","NM_001378454.1","ENST00000613296.6","-","YES","1/23","-","NM_001378454.1:c.39_41dup","NP_001365383.1:p.Glu27dup","rs764804760;rs72319667;rs778948871;rs3074417;rs61156725;rs193922695","rs764804760;rs72319667;rs778948871;rs3074417;rs61156725;rs193922695","-","MODERATE","inframe_insertion","-","-","-","-","-","0,3122","0,3242","0,6335","gnomADg_AMI","69-74/12844","36-41/12507","12-14/4168","LEE/LEEE","ctGGAGGAg/ctGGAGGAGGAg","-","1","-","1","TGGAGGA","T,TGGAGGAGGA","5","133","0,3122","0,08531","0,294","0,3211","0,4178","0,3064","0,3419","0,3187","NM_001378454.1","-","4191-25-HLUCHOTA50-F_chr2_73385903_TGGAGGA_T,TGGAGGAGGA","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","2/3","66,67" +"4191-25-HLUCHOTA50-F","2/3","66,67","452","54,65","ALMS1","chr2","HET","SNV","73386213","NM_001378454.1","ENST00000613296.6","-","YES","-","1/22","NM_001378454.1:c.324+21G>A","-","rs11126399","rs11126399","-","MODIFIER","intron_variant","-","-","-","-","-","0,2795","0,3072","0,3072","gnomADe_NFE","-","-","-","-","-","-","1","0&1","1&1","G","A","205","247","0,2795","0,2841","0,2449","0,2641","0,2363","0,2992","0,2819","0,2697","NM_001378454.1","-","4191-25-HLUCHOTA50-F_chr2_73386213_G_A","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","benign","2/3","66,67" +"4191-25-HLUCHOTA50-F","3/3","100","102","47,06","ALMS1","chr2","HET","SNV","73422994","NM_001378454.1","ENST00000613296.6","-","YES","-","4/22","NM_001378454.1:c.764+20T>A","-","rs1881246","rs1881246","-","MODIFIER","intron_variant","-","-","-","-","-","0,6069","0,6295","0,7877","EAS","-","-","-","-","-","-","1","0&1","1&1","T","A","54","48","0,6069","0,1802","0,5448","0,6604","0,7788","0,6098","0,6268","0,6845","NM_001378454.1","-","4191-25-HLUCHOTA50-F_chr2_73422994_T_A","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","benign","3/3","100" +"4191-25-HLUCHOTA50-F","1/3","33,33","343","45,48","ALMS1","chr2","HET","SNV","73424839","NM_001378454.1","ENST00000613296.6","-","YES","5/23","-","NM_001378454.1:c.1174C>T","NP_001365383.1:p.Arg392Cys","rs3813227","rs3813227","-","MODERATE","missense_variant","Benign","tolerated","1","benign","0","0,2658","0,2364","0,8782","AFR","1207/12844","1174/12507","392/4168","R/C","Cgt/Tgt","-","1","-","1","C","T","187","156","0,2658","0,7838","0,407","0,1729","0,006143","0,2322","0,2417","0,1609","NM_001378454.1","-","4191-25-HLUCHOTA50-F_chr2_73424839_C_T","-","-","-","-","-","-","-","-","-","-","-","383753","NC_000002.12:g.73424839C>T","Cardiovascular_phenotype&Alstrom_syndrome¬_specified","criteria_provided&_multiple_submitters&_no_conflicts","benign","1/3","33,33" +"4191-25-HLUCHOTA50-F","2/3","66,67","155","51,61","ALMS1","chr2","HET","deletion","73448097","NM_001378454.1","ENST00000613296.6","-","YES","8/23","-","NM_001378454.1:c.1574_1576del","NP_001365383.1:p.Pro525del","rs797045227","rs797045227","-","MODERATE","inframe_deletion","-","-","-","-","-","-","-","0,6384","gnomADg_AFR","1604-1606/12844","1571-1573/12507","524-525/4168","SP/S","tCTCct/tct","-","1","-","1","TCTC","T","75","80","-","-","-","-","-","-","-","-","NM_001378454.1","-","4191-25-HLUCHOTA50-F_chr2_73448097_TCTC_T","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","2/3","66,67" 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+"4191-25-HLUCHOTA50-F","3/3","100","314","50,64","ALMS1","chr2","HET","SNV","73448717","NM_001378454.1","ENST00000613296.6","-","YES","8/23","-","NM_001378454.1:c.2190C>T","NP_001365383.1:p.Phe730=","rs7598901","rs7598901","-","LOW","synonymous_variant","-","-","-","-","-","0,6029","0,6289","0,7798","EAS","2223/12844","2190/12507","730/4168","F","ttC/ttT","-","1","0&1","1&1","C","T","155","159","0,6029","0,1801","0,5447","0,6275","0,7771","0,6098","0,6236","0,6675","NM_001378454.1","-","4191-25-HLUCHOTA50-F_chr2_73448717_C_T","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","benign","3/3","100" +"4191-25-HLUCHOTA50-F","1/3","33,33","370","52,7","ALMS1","chr2","HET","SNV","73450706","NM_001378454.1","ENST00000613296.6","-","YES","8/23","-","NM_001378454.1:c.4179A>G","NP_001365383.1:p.Gln1393=","rs6546836","rs6546836","-","LOW","synonymous_variant","-","-","-","-","-","0,2593","0,2361","0,7859","AFR","4212/12844","4179/12507","1393/4168","Q","caA/caG","-","1","0&1","1&1","A","G","175","195","0,2593","0,7131","0,4033","0,151","0,006066","0,233","0,2367","0,1602","NM_001378454.1","-","4191-25-HLUCHOTA50-F_chr2_73450706_A_G","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","benign","1/3","33,33" 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setdiff(expected_columns, output_columns) + extra_columns <- setdiff(output_columns, expected_columns) + expect_true(rlang::is_empty(missing_columns), info = glue("Missing column in output Finalist columns: {missing_columns}")) + expect_true(rlang::is_empty(extra_columns), info = glue("Extra column in output Finalist columns: {extra_columns}")) + + finalist_df <- finalist_df[, intersect(colnames(expected_finalist_df), colnames(finalist_df))] expect_true(all.equal(expected_finalist_df, finalist_df)) }