Table 1. Basic usage examples of the grep, awk, and sed commands.

Command	Example	Description
grep	grep "chr5" file	Print all lines that contain the string "chr5" in the named file
awk	awk '$1 == 5 {print $2, $3}' file	For rows in the named file where the value in column 1 is equal to 5, print columns 2 and 3
sed	sed 's/sample1/ID7037/g’ file	Replace all occurrences of "sample1" with "ID7037" in the named file and print the result