Prepare Input Files

GWAS summary statistics for a genetic locus of interest

Overview

To perform a QTLs analysis on FUMA, a GWAS summary statistics for a genetic locus of interest is required.
The file has to have the following columns in this specific order: CHR, POS, REF, ALT, N, BETA, P, MAF.
Delimiter is a tab character.
The file is not zipped.
The file size needs to be less than 10Mb. Because this file is subsetted for a single genomic risk locus, this file should be relatively small.
Tips: write a script in R or Python to
- Subset the full GWAS summary statistics using the start and end coordinates that represent a genetic locus of interest
- Select the 8 columns: CHR, POS, REF, ALT, N, BETA, P, MAF
Example code:

outfile = open("locus.input", "w")
header = ["CHR", "POS", "REF", "ALT", "N", "BETA", "P", "MAF"]
print("\t".join(header), file=outfile)

locus_chrom = {chrom} #replace with the chromosome from the genetic locus of interest
start = {start} #replace with the start coordinates from the genetic locus of interest
end = {end} #replace with the end coordinates from the genetic locus of interest

with open({input}, "r") as f: #replace with the path to the GWAS summary statistics
    for line in f:
        if line.startswith("variant_id"): #replace with the correct value to skip header line if needed
            continue  # skip header line
        items = line.rstrip("\n").split("\t") #replace with the correct delimiter
        chrom = items[1] #replace with the correct index
        pos = items[2] #replace with the correct index
        if chrom == locus_chrom and int(pos) >= start and int(pos) <= end:
            alt = items[4] #replace with the correct index
            ref = items[3] #replace with the correct index
            n_samples = items[7] #replace with the correct index
            beta = items[6] #replace with the correct index
            p = items[8] #replace with the correct index
            maf = items[5] #replace with the correct index
            print("\t".join([chrom, pos, ref, alt, n_samples, beta, p, maf]), file=outfile)
outfile.close()

Tip

Use a programming language such as R or Python to prepare your input file

Example input file:

CHR     POS     REF     ALT     N       BETA    P       MAF
     25243213        G       A       716517  0.0621  5.534e-07       0.6976
     25243984        G       A       716517  -0.0175 0.7148  0.9827
     25244245        G       A       716517  -0.0391 0.5636  0.9888
     25244270        G       C       716517  0.0257  0.03354 0.3088
     25244326        C       A       716517  0.0256  0.03399 0.3090