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#NOTE: The homoplasmic_variants.txt file should be uploaded into your folder (directory) in the SCC cluster.

#NOTE: Save the excel file as Merged_QC.csv. 

Homoplasmy and heteroplasmy – transition and transversion rates.

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1. Copy the entire data from the homoplasmy_only tab (from Merged_QC.txt csv file) and paste it into a new excel file. Next, follow the steps described below:.
2. First, name the 1^st tab as homoplasmic_variants. The first tab contains the total number of variants (number of rows). Take a side note of the total number of variants you have.
3. Create a 2^nd tab and call it as unique_homoplasmic_variants. Copy and paste the entire data from the 1st sheet into the 2nd and exclude all the duplicate variants, this way you are going to keep only unique/bi-allelic variants. Take a side note of the number of unique variants you have at this step. 

#NOTE: Check out at the end of this section an example of how the excel file was organized in different sheets based on the QC steps (Figure 2).

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