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module load bio/PLINK2/20210420-x86_64
plink2 --vcf work_directory_path/Merged.vcf.gz --double-id --max-alleles 2 --vcf-half-call haploid  --make-bed --out Workshop_samples-_05-17-23

#NOTE: After running the command above you need to ensure that you got 4 different files called Workshop_samples-05-17-23.bed, Workshop_samples-05-17-23.bim, Workshop_samples-05-17-23.fam and Workshop_samples-05-17-23.log.


awk '{print $1, $1'MT-'$4, $3, $4, $5, $6}' Workshop_samples
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_05-17-23.bim > Workshop_samples
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_05-17-23_nv.bim