Introduction to Linux Command | Extract, Sort & Find Unique Values using cut, sort, and uniq
The cut, sort, and uniq commands are essential text-processing tools in Linux and Unix-like systems. Together, they allow you to extract specific columns from structured data, organize the output, and identify unique values—all from the command line.
In this tutorial, you'll learn how to combine these commands into a simple yet powerful pipeline to analyze genomics data stored in CSV files. Whether you're working in bioinformatics, data science, or Linux system administration, these commands will help you efficiently process large datasets without using spreadsheets.
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Understanding the Pipe (|) to learn how command pipelines work before trying this exercise.
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Command demonstrated:
cat *_ variants.csv | cut -d "," -f 2 | sort | uniq
What you'll learn:
✅ How to extract a specific column from a CSV file using cut
✅ Why is sorting required before using uniq
✅ How to identify unique genomic variants from multiple files
✅ Building efficient Linux command-line pipelines for bioinformatics data analysis
✅ Practical examples using real genomics datasets
Shell Challenge
Can you extend this pipeline to answer the following questions?
1. Can you find the lines that do not match a pattern? How can you remove the header line from your output?
2. What happens when you replace uniq with uniq -c? What does the output represent?
3. Can you create a sorted table showing the count of each variant in descending numerical order, with the most common variant at the top?
💡 Hint: Use man grep and man uniq to discover the options you'll need.
This tutorial is part of the HeliOmics Linux & Bioinformatics Series, designed to help researchers, students, and professionals become more confident with Linux, shell scripting, and computational biology workflows.
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