DECIMAT

Pyhton script to filter loci from Eigenstrat files (.snp & .geno) keeping the overall structure of the triad

Filter SNPs from Eigenstrat files based on various criteria. Usage: python decimat.py --input_prefix prefix --output_prefix filtered_prefix [options]

Options examples:

Filter to keep specific chromosomes

python decimat.py -i input_data -o filtered_data -c 1 2 3

Filter to keep position range on chromosome 1

python decimat.py -i input_data -o filtered_data -r 1:1000000-2000000

Filter to keep SNP list file

python decimat.py -i input_data -o filtered_data -s keep_snps.txt

Filter to keep regex pattern (keep only rs IDs)

python decimat.py -i input_data -o filtered_data -p "^rs[0-9]+$"

Combine multiple filters to keep certain SNPs

python decimat.py -i input_data -o filtered_data -c 1 2 3 -r 1:500000-1500000 -p "rs"