# Rename columns
RENAME	SNPID	rsId
RENAME	chr	chrom
RENAME	position	bp
RENAME	SE	StdErr
RENAME	pval	p-value
RENAME	p	p-value
RENAME	pvalue	p-value

# Column names: specify the meaning of every column in the input file
ALLELE		coded_all noncoded_all
CALLRATE 	callrate
CHR		chrom
EFFECT 		beta
FREQLABEL 	AF_coded_all 
HWE_PVAL 	HWE_pval
IMPUTED 	imputed
IMP_QUALITY 	oevar_imp
MARKER		rsId
N 		n_total
POSITION 	bp
PVALUE 		p-value
STRAND 		strand_genome
STDERR 		StdErr
USED_FOR_IMP 	used_for_imp
AVPOSTPROB	avpostprob

# Prefix for output files
PREFIX	pgwasformat_

# Enable computation of inflation factor and genomic control
GC	ON

# Set filters on minor allele frequency and imputation quality
HQ_SNP	0.05 0.4

# Enable column re-ordering and specify the order explicitely
ORDER	ON	chrom bp rsId strand_genome coded_all noncoded_all AF_coded_all callrate HWE_pval imputed used_for_imp avpostprob oevar_imp n_total n_total_effective p-value p-value_gc beta StdErr StdErr_gc 

# Input file and its short name for labels
PROCESS gwa_data_example_1.txt Study1

# Enable column re-ordering based on the alphabetical ordering
ORDER	ON

# Disable filters
HQ_SNP	0 0

PROCESS gwa_data_example_2.tbl Study2
PROCESS gwa_data_example_3.csv Study3

# Disable column re-ordering
ORDER	OFF

PROCESS gwa_data_example_4.txt Study4
PROCESS gwa_data_example_5.csv Study5