A GWAS file is a space- or tab-delimited result file from genome-wide association study (GWAS) analysis. These files include PLINK result files containing integrated map information (i.e., chromosomal location for each association).

File extensions for GWAS files are: .linear, .logistic, .assoc, .qassoc, .gwas

GWAS file must contain four columns (case-insensitive):

  • CHR: chromosome (aliases chr, chromosome)
  • BP: nucleotide location (aliases bp, pos, position)
  • SNP: SNP identifier (aliases snp, rs, rsid, rsnum, id, marker, markername)
  • P: p-value for the association (aliases p, pval, p-value, pvalue, p.value)

Columns can be in any order.  Other columns besides the required ones are allowed.  The file must be sorted by start position in ascending order.   The p-value will be transformed to -log10 scale for plotting.