Created
August 6, 2019 11:35
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| # 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 |
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