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Filtering out the samples that were contaminated

• To filter out the contaminated samples we will use the file samples_to_remove.txt created in previous steps on the QC section. Verify if you have already uploaded this file into the work directory and run the commands described below.

module load bio/PLINK/1.9b_6.22-x86_64
plink --bfile Workshop_samples_05-17-23_nv --remove samples_to_remove.txt --make-bed --out Workshop_samples_05-17-23_nocont

#NOTE: The samples_to_remove.txt file was created at on the QC section.

Homoplasmic variants calling

• For this part of the analysis, you are going to call only the homoplasmic variants by using the homoplasmic_variants.txtfile. This file was created in the section Quality Control (QC) steps, step 5. Before continuing, you must certify that the homoplasmic_variants.txtfile was uploaded into your work directory in the SCC cluster. Next, run the analysis by using the commands described below.

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