Usage

Run

./main.sh [ required args ] [ optional args ]

Results will be saved in results file, with the following headers:

SNP CHR BP START GENE STRAND A1 A2 FREQ B B_C SE SE_C P P_C P_T N TYPE ROUND

Required files:

gcta64 binary in this directory (otherwise specify path in definitions/contants.sh)

Input file (SNPs of interest)

Bfiles (.bed, .bim, .fam)

Arguments:

Required:

--infile - input file
--bfile - bed file
--chr - chromosome number
--maf - minor allele frequency

Optional:

--genes - file with subset of genes to run GCTA-COJO for (Row format) (gene_list by default)
--gene_dir - directory name where gene .ma files will be saved (cojo_files by default)
--run-dir - directory name where all the files will be saved (run_$date by default)
--log - log file name ($date.log by default)
--p_val - p-value threshold (value or "per_chr" or "per_gene")
--snps - file with subset of SNPs to run GCTA-COJO for (Row format)

Files

main.sh - main file which should be executed by the user

transform.sh - transforms infile (input file) into a .ma file for each gene

run.sh - runs GCTA-COJO iteratively for each SNP

definitions/constants.sh - stores constants, such as the default p-value

definitions/file_indices.sh - stores input (GWAS summary statistics), .ma, .cma.cojo column indices

definitions/functions.sh - stores logging functions' declarations

definitions/log_messages.sh - stores log messages