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- 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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- (see the image below as an example).
#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 file has two columns containing the same Sample ID in both columns and no header.
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