# VCF file = test.filt.vcf.gz
# replace where necessary

(printf "chr\npos\nref\n"; bcftools query -l test.filt.vcf.gz) | datamash transpose > test.filt.mat.bin
bcftools query -f '%CHROM\t%POS\t%REF[\t%GT]\n' test.filt.vcf.gz | tr '|' '/' | sed 's/\.\/\./N/g' | sed 's/0\/0/0/g' | sed 's/.\/./1/g' >> test.filt.mat.bin