...

Homoplasmic and common variants filtering using PLINK in the SCC cluster

Converting vcf to plink files

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.

• IMPORTANT! Before continuing the analysis, you will need to edit your .bim file by adding the preposition MT- plus the variant location in the second column. For that, you can use the command described below.

awk '{print $1, $1'MT-'$4, $3, $4, $5, $6}' Workshop_samples_05-17-23.bim > Workshop_samples_05-17-23_nv.bim

• After running the command above, I suggest you verify if the new file file_name_outputbim has the MT- added to the variant's position in column 2. For that, you can use the command below.

vi Workshop_samples_05-17-23_nv.bim
ESC :wq

Homoplasmic variants calling