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Use the excel to open the files Merged.txt, haplocheck_results (contains the contamination status), andhaplogroups_workshopsamples.txt (contains the haplogroup information for each one of the samples).

1.  By using the haplocheck_results file, you will check which samples are contaminated (column B: Contamination Status). If there is any sample indicating YES in the contamination status column you will need to copy the Sample IDs (column A: Sample) and paste in a new excel file. Name your file as samples_to_remove and save it as txt format.

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#NOTE:If is written YES in the column B, it means that the sample is contaminated based on differences between Major and Minor haplogroups.

#NOTE: samples_to_remove.txt has two columns containing the Sample ID in both columns.

Homoplasmic and common variants filtering using PLINK in the SCC cluster

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