The script below is an attempt to combine 3 shells into 1.
The first part: match.sh
prompts the user for an id of a patient and runs a match script based on the response of "y" or "n". After completing the user is asked if there are additional patients, and based on "y" or "n" a certain action is followed.
The second part: convert2annovar.sh
prompts the user for an id of a patient and runs a conversion script based on the response of "y" or "n". After completing the user is asked if there are additional patients, and based on "y" or "n" a certain action is followed.
The third part: table_annovar
prompts the user for the type of analysis and runs a script based on the response of "y" or "n". After completing the user is asked if there are additional patients, and based on "y" or "n" a certain action is followed.
I attached the .sh file as well. Thank you
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