Loading required namespace: GenomicFiles Using local VCF. File already tabix-indexed. Finding empty VCF columns based on first 10,000 rows. Dropping 1 duplicate column(s). 1 sample detected: ieu-b-4874 Constructing ScanVcfParam object. VCF contains: 9,904,926 variant(s) x 1 sample(s) Reading VCF file: multi-threaded (4 threads) Dropping 1 duplicate column(s). Dropping 1 duplicate column(s). Dropping 1 duplicate column(s). Dropping 1 duplicate column(s). Renaming ID as SNP. VCF file has -log10 P-values; these will be converted to unadjusted p-values in the 'P' column. Renaming SI column as INFO. Formatting INFO column. Standardising column headers. First line of summary statistics file: SNP chr BP end REF ALT FILTER AF ES LP SE INFO P Summary statistics report: - 9,801,461 rows - 9,627,715 unique variants - 5 genome-wide significant variants (P<5e-8) - 22 chromosomes Checking for multi-GWAS. Checking for multiple RSIDs on one row. Inferring genome build. Loading SNPlocs data. Loading reference genome data. Preprocessing RSIDs. Validating RSIDs of 10,000 SNPs using BSgenome::snpsById... Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: expand.grid, I, unname BSgenome::snpsById done in 25 seconds. Loading SNPlocs data. Loading reference genome data. Preprocessing RSIDs. Validating RSIDs of 10,000 SNPs using BSgenome::snpsById... BSgenome::snpsById done in 39 seconds. Inferred genome build: GRCH37 Checking SNP RSIDs. Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-4874/logs/snp_missing_rs.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-4874/logs/snp_multi_colon.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. 968 SNP IDs appear to be made up of chr:bp, these will be replaced by their SNP ID from the reference genome Loading SNPlocs data. Found Indels. These won't be checked against the reference genome as it does not contain Indels. WARNING If your sumstat doesn't contain Indels, set the indel param to FALSE & rerun MungeSumstats::format_sumstats() Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-4874/logs/snp_not_found_from_bp_chr.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. Checking for merged allele column. Checking A1 is uppercase Checking A2 is uppercase Checking for incorrect base-pair positions Ensuring all SNPs are on the reference genome. Loading SNPlocs data. Loading reference genome data. Preprocessing RSIDs. Validating RSIDs of 9,627,039 SNPs using BSgenome::snpsById... BSgenome::snpsById done in 109 seconds. Found 1,137,296 Indels. These won't be checked against the reference genome as it does not contain Indels. WARNING If your sumstat doesn't contain Indels, set the indel param to FALSE & rerun MungeSumstats::format_sumstats() Checking for correct direction of A1 (reference) and A2 (alternative allele). There are 113 SNPs where neither A1 nor A2 match the reference genome. These will be removed. Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-4874/logs/alleles_dont_match_ref_gen.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. There are 7,575 SNPs where A1 doesn't match the reference genome. These will be flipped with their effect columns. Reordering so first three column headers are SNP, CHR and BP in this order. Reordering so the fourth and fifth columns are A1 and A2. Checking for missing data. Checking for duplicate columns. Checking for duplicate SNPs from SNP ID. Found 15,920 Indels. These won't be checked for duplicates based on RS ID as there can be multiples. WARNING If your sumstat doesn't contain Indels, set the indel param to FALSE & rerun MungeSumstats::format_sumstats() 4,767 RSIDs are duplicated in the sumstats file. These duplicates will be removed Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-4874/logs/dup_snp_id.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. Checking for SNPs with duplicated base-pair positions. Found 15,920 Indels. These won't be checked for duplicates based on base-pair position as there can be multiples. WARNING If your sumstat doesn't contain Indels, set the indel param to FALSE & rerun MungeSumstats::format_sumstats() Checking for duplicated rows. 3 sumstat rows are duplicated. These duplicates will be removed. Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-4874/logs/dup_row.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. Filtering SNPs based on INFO score. 371,057 SNPs are below the INFO threshold of 0.9 and will be removed. Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-4874/logs/info_filter.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. Filtering SNPs, ensuring SE>0. Ensuring all SNPs have N<5 std dev above mean. Checking for bi-allelic SNPs. 182,549 SNPs are non-biallelic. These will be removed. Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-4874/logs/snp_bi_allelic.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. Computing Z-score from P using formula: `sign(BETA)*sqrt(stats::qchisq(P,1,lower=FALSE)` Warning: When method is an integer, must be >0. 1,355,865 SNPs (18.9%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency. The FRQ column was mapped from one of the following from the inputted summary statistics file: FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency, set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency. Sorting coordinates with 'data.table'. Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-4874/ieu-b-4874.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. Summary statistics report: - 7,172,437 rows (73.2% of original 9,801,461 rows) - 7,172,204 unique variants - 4 genome-wide significant variants (P<5e-8) - 22 chromosomes Done munging in 15.76 minutes. Successfully finished preparing sumstats file, preview: Reading header. SNP CHR BP A1 A2 END FILTER FRQ BETA LP 1: rs12184267 1 715265 C T 715265 PASS 0.036838 0.000381578 0.508638 2: rs12184277 1 715367 A G 715367 PASS 0.036946 0.000371035 0.481486 3: rs12184279 1 717485 C A 717485 PASS 0.036652 0.000328581 0.408935 4: rs116801199 1 720381 G T 720381 PASS 0.037203 0.000388079 0.522879 5: rs12565286 1 721290 G C 721290 PASS 0.037293 0.000365232 0.481486 SE INFO P Z 1: 0.000379212 0.931195 0.3100002 1.0152216 2: 0.000377811 0.935480 0.3300000 0.9741138 3: 0.000380481 0.929419 0.3900004 0.8596167 4: 0.000376217 0.937047 0.2999998 1.0364338 5: 0.000374958 0.941252 0.3300000 0.9741138