...
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).
Filtering out variants from samples identified as contaminated
- By First, to identify the samples that are contaminated we will be using the haplocheck_results file. For that, you will check which samples are contaminated (check the column B : Contamination (Contaminated Status) . If and verify if there is any sample indicating YES in the contamination status column. If , 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 (see the image below as an example).
...