# Description (meaning) of the columns in input files 
# with GWAS data to be annotated.
MARKER		SNPID
CHR		chr
POSITION	position

# File with regions.
REGIONS_FILE	genes_HGNC_ensembl_rel54_may2009_b36.txt

# Description (meaning) of the columns in file with regions.
REGION_NAME	Gene
REGION_CHR	Chromosome
REGION_START	Start
REGION_END	End

# Window sizes around markers.
REGIONS_DEVIATION	0 10000 25000

# Preserve original columns in the output file and append 
# columns with annotated regions to the end.
REGIONS_APPEND	ON

# Specify prefix for output files with annotation results.
PREFIX		pannotated_

# Input file with GWAS data to annotate.
PROCESS		gwa_data_example_1.txt

# Next file with GWAS data will be annotated using marker 
# chromosomal positions in the external map file.
MAP_FILE	map_b37.txt

# Description (meaning) of the columns in map file.
MAP_MARKER	snpid
MAP_CHR		chr_b37
MAP_POSITION	pos_b37

# Change the regions file.
REGIONS_FILE	genes_HGNC_ensembl_rel67_may2012_b37.txt

# Change window sizes around markers.
REGIONS_DEVIATION	0 25000 50000

# Output only columns with annotated regions, marker 
# names and their chromosomal positions.
REGIONS_APPEND	OFF

# Another input file with GWAS data to annotate.
PROCESS		gwa_data_example_2.tbl 