generate GRMs for each chromosome

alspac_grm_chr.sh

#!/bin/bash

for i in {1..9}
do
	plink1.90 --bfile ~/data/alspac_1kg/data/genotypes/bestguess/subset_maf0.01_info0.8/data_chr0${i} --extract ~/data/1kg_scratch/hapmap3_autosome.snplist --make-grm-bin --out data_chr0${i} --maf 0.01
done

for i in {10..22}
do
	plink1.90 --bfile ~/data/alspac_1kg/data/genotypes/bestguess/subset_maf0.01_info0.8/data_chr${i} --extract ~/data/1kg_scratch/hapmap3_autosome.snplist --make-grm-bin --out data_chr${i} --maf 0.01
done