Question about sed command in Run-plink.sh modification

[cykim-saihst]

Hi,

I noticed that the setup includes the following command:
sed -i 's/--recode vcf/--recode vcf --output-chr chrM/g' Run-plink.sh

Could you clarify the purpose of adding --output-chr chrM to all --recode vcf commands in Run-plink.sh?
Since --output-chr chrM is typically used to modify the naming of mitochondrial chromosomes, I wanted to check whether this is necessary for all chromosomes or if it's intended only for mitochondrial data.

Thank you!