I am using putty to run plink for this data analysis.
I have been asked to perform a QC on a subset of data from a given dataset. I have used the command to keep the data (plink --bfile data --keep mydata.txt) and it has saved the necessary files as a .txt file.
When I enter (plink --file mydata --maf 0.05) it states that no mydata.ped file exists?
How do I overcome this problem?