Bioinformatics Terminal Command Cheat Sheet

Essential Linux, Vim, awk, and HPC commands for genomic data workflows

Bash

AWK

Command Line

Data Science

A quick-reference guide to the terminal commands used most often when inspecting, filtering, and processing sequencing and variant data.

Author

Nivedita Bhadra

Published

July 10, 2025

Diagram of a terminal running common bioinformatics commands, alongside badges for FASTQ, VCF, BAM, and HPC/SLURM workflows

The core command families this cheat sheet covers: file inspection, pattern matching, column processing, and job management on an HPC cluster.

Bioinformatics workflows almost always come down to the terminal: inspecting sequencing files, filtering variant calls, and shepherding jobs through an HPC queue. This cheat sheet collects the commands reached for most often across those tasks — from basic Linux navigation to awk/grep one-liners for VCF files and SLURM job management. Everything below is copy-paste ready.

Linux/Unix Shell awk grep SLURM/HPC

1 Basic Linux Commands

cd <path/to/dir> – Change working directory
pwd – Print working directory
ll (alias for ls -l) – Show the contents of the current directory as a list
head -n X <filename> – Print the first X lines of a file
cat <filename> – Print the full content of a file
less <filename> – Display the file and scroll through lines (exit by pressing q)
zcat <filename.gz> | head – Print the head of a .gz file (pipes full content to head)
cp <from_file.xyz> <to_file.xyz> – Copy a file from one location to another
mv <old_file.xyz> <new_file.xyz> – Move a file (also used for renaming)
rm <file> – Remove a file
rmdir <directory_name> – Remove a directory (must be empty)
mkdir <directory_name> – Make a new directory
grep <pattern> <filename> – Print lines in a file containing a pattern
find . -name "*.txt" – Search for files in the current directory matching *.txt
nano <file> – Open the Nano text editor to create or edit files
find /path/to/folder -type f | wc -l - Count the total number of files in a specific folders.
ls | head -20 – Show the first 20 files in the current folder
ls | tail -20 – Show the last 20 files in the current folder
ls -lt | head -20 – Show the 20 most recently modified files
ls -ltr | head -20 – Show the 20 oldest files (by modification time)
ls -1 | wc -l – Count the total number of files in the directory
ls -a | head -20 – Show the first 20 files, including hidden files (those starting with .)
ls -d $PWD/* | head -20 – Show the first 20 files with full pathnames
du -sh * – Show the size of all files and folders in the current directory (human-readable format)
du -sh <folder_name> – Display the size of a specific folder
du -sh . – Show the total size of the current directory
du -sh * | sort -h – Sort files and folders by size (smallest to largest)
du -sh * | sort -hr | head -20 – Show the 20 largest files/folders in the current directory
ls -lhS | head -20 – Show the 20 largest files in the current directory
find . -type f -exec du -h {} + | sort -hr | head -20 – List the 20 largest files recursively in current and subdirectories
df -h – Display disk space usage for all mounted file systems (human-readable format)
df -h /path/to/dir – Show available disk space for a specific directory path

1.1 One-Liner: Counting Folders Missing Compressed Files

A common HPC hygiene check — scanning a batch of result folders (e.g. GWAS summary statistics) for any that are missing their expected .gz output:

count=0
for dir in sumstats_FG*/; do
    if ! ls "$dir"/*.gz >/dev/null 2>&1; then
        echo "No .gz file in: $dir"
        ((count++))
    fi
done
echo "Total folders without .gz files: $count"

2 Basic Vim Commands

vim <filename> – Open a file in Vim (creates it if it doesn’t exist)
i – Switch to Insert mode (to start editing text)
Esc – Exit Insert mode and return to Normal mode
:w – Save (write) the file
:q – Quit Vim
:wq – Save and quit Vim
:q! – Quit without saving changes
x – Delete the character under the cursor
dd – Delete the current line
yy – Yank (copy) the current line
p – Paste the copied or deleted text below the cursor
/pattern – Search forward for a pattern in the file
n – Repeat the last search in the same direction
u – Undo the last action
Ctrl + r – Redo an undone action
gg – Go to the beginning of the file
G – Go to the end of the file

3 Searching with `grep`

grep "ACTG" <filename> – Find lines containing ACTG
grep -v "N" <filename> – Exclude lines with “N”
grep -c "rs" <filename> – Count lines with “rs”
grep -w "chr1" <filename> – Match whole word “chr1”
zgrep "chr1" <filename>.vcf.gz – Grep inside gzipped VCF file

4 Column Operations with `awk`

awk '{print $1}' <filename> – Print 1st column
awk '$5 > 0.05' <filename> – Filter rows with 5th column > 0.05
awk 'NR>1' <filename> – Skip header (first row)
awk 'BEGIN{FS="\t"} {print $2,$3}' <filename> – Tab-delimited input

5 Working with `.vcf.gz` Files

zcat file.vcf.gz | head
Shows the top lines including headers and first few variants
zcat file.vcf.gz | tail
Shows the last few lines — useful for trailing info
zcat file.vcf.gz | grep '^#'
Shows all header lines (metadata + column names)
zcat file.vcf.gz | grep -v '^#'
Skips headers and shows actual variant records
zcat file.vcf.gz | grep -v '^#' | cut -f10 | head
Displays the contents of the FORMAT/sample column
zcat file.vcf.gz | grep -v '^#' | wc -l
Counts the number of data (variant) rows
zcat file.vcf.gz | grep -m1 '^#CHROM' | cut -f9
Extracts FORMAT field labels (e.g., ES:SE:EP:AF:AFKG)
zcat file.vcf.gz | grep -v '^#' | awk 'NR <= 5 { print $3, $4, $5 }'
Prints rsID, REF, and ALT for the first 5 variants

6 Finding Files with `find`

find . -name "*.vcf" – Find all .vcf files
find /data -type f -size +1G – Files >1GB in /data
find . -mtime -1 – Modified in last 24 hrs
find . -exec grep "rs123" {} \; – Search “rs123” in all files
find . -mindepth 1 -maxdepth 1 -type d | wc -l - Count the number of folder inside a folder
find . -name "filename.txt" – Search for a file named filename.txt in the current directory and subdirectories
find /path/to/search -name "filename.txt" – Search for a file in a specific directory path
find / -name "filename.txt" 2>/dev/null – Search the entire system (suppress “Permission denied” errors)
locate filename.txt – Quickly search for a file using the system’s file index (requires mlocate or plocate installed)
find . -iname "filename.txt" – Case-insensitive search for the file name

7 Text Processing Essentials

cut -f1,3 <filename> – Cut fields 1 and 3
sort <filename> – Sort lines
sort -k2,2n <filename> – Sort by 2nd column numerically
uniq -c <filename> – Count unique lines
paste <file1> <file2> – Merge files side by side
wc -l <filename> – Count lines in a file

8 Genomic Data Tools

samtools view <file>.bam – View alignment data
bcftools view <file>.vcf.gz – View VCF data
bedtools intersect -a <a.bed> -b <b.bed> – Genomic region overlap
plink --bfile <data> --assoc – Run basic association test

9 Common HPC command

srun --time=02:00:00 --mem=8G --cpus-per-task=2 --pty bash – Start an interactive session on the HPC
squeue – View the job queue
squeue -u <user_id> – View jobs from a specific user
squeue --help – View additional options for squeue
sacct -j <job_id> – Get the status of a specific job
scontrol show job <job_id> – View extended information for a specific job
seff <job_id> – View running jobs with estimated CPU usage efficiency
scancel <job_id> – Cancel a specific job
scancel -u <user_id> – Cancel all running jobs for a user
sinfo -N – View the current load on the queuing system
squeue --states=PENDING – Show only pending jobs in the queue
squeue -u <user_id> --states=PD – Show only your pending jobs
squeue | grep PD | wc -l – Count how many jobs are pending system-wide
squeue -u <user_id> | grep PD | wc -l – Count how many of your jobs are pending

10 Next Steps

These commands cover the majority of day-to-day file inspection and job management, but a few directions are worth exploring next: writing small awk/bash scripts to automate recurring QC checks, learning sbatch for submitting batch (non-interactive) HPC jobs, and using tmux or screen to keep long-running sessions alive after disconnecting.

sbatch tmux Shell Scripting QC Automation

--- title: "Bioinformatics Terminal Command Cheat Sheet" subtitle: "Essential Linux, Vim, awk, and HPC commands for genomic data workflows" description: "A quick-reference guide to the terminal commands used most often when inspecting, filtering, and processing sequencing and variant data." author: "Nivedita Bhadra" date: 2025-07-10 image: images/bioinformatics-commands.svg categories: - Bash - AWK - Command Line - Data Science format: html: toc: true toc-depth: 3 code-tools: true code-fold: false code-copy: true code-overflow: wrap number-sections: true reading-time: true page-layout: article execute: echo: true warning: false message: false --- ::: {.thesis-hero-wrap} <img src="images/bioinformatics-commands.svg" alt="Diagram of a terminal running common bioinformatics commands, alongside badges for FASTQ, VCF, BAM, and HPC/SLURM workflows" class="thesis-hero-art"/> ::: {.thesis-hero-caption} The core command families this cheat sheet covers: file inspection, pattern matching, column processing, and job management on an HPC cluster. ::: ::: Bioinformatics workflows almost always come down to the terminal: inspecting sequencing files, filtering variant calls, and shepherding jobs through an HPC queue. This cheat sheet collects the commands reached for most often across those tasks — from basic Linux navigation to `awk`/`grep` one-liners for VCF files and SLURM job management. Everything below is copy-paste ready. ::: {.tag-row} [Linux/Unix Shell]{.tag} [awk]{.tag} [grep]{.tag} [SLURM/HPC]{.tag} ::: --- ## Basic Linux Commands - `cd <path/to/dir>` – Change working directory - `pwd` – Print working directory - `ll` (alias for `ls -l`) – Show the contents of the current directory as a list - `head -n X <filename>` – Print the first X lines of a file - `cat <filename>` – Print the full content of a file - `less <filename>` – Display the file and scroll through lines (exit by pressing `q`) - `zcat <filename.gz> | head` – Print the head of a `.gz` file (pipes full content to `head`) - `cp <from_file.xyz> <to_file.xyz>` – Copy a file from one location to another - `mv <old_file.xyz> <new_file.xyz>` – Move a file (also used for renaming) - `rm <file>` – Remove a file - `rmdir <directory_name>` – Remove a directory (must be empty) - `mkdir <directory_name>` – Make a new directory - `grep <pattern> <filename>` – Print lines in a file containing a pattern - `find . -name "*.txt"` – Search for files in the current directory matching `*.txt` - `nano <file>` – Open the Nano text editor to create or edit files - `find /path/to/folder -type f | wc -l` - Count the total number of files in a specific folders. - `ls | head -20` – Show the **first 20 files** in the current folder - `ls | tail -20` – Show the **last 20 files** in the current folder - `ls -lt | head -20` – Show the **20 most recently modified files** - `ls -ltr | head -20` – Show the **20 oldest files (by modification time)** - `ls -1 | wc -l` – Count the **total number of files** in the directory - `ls -a | head -20` – Show the first 20 files, including hidden files (those starting with `.`) - `ls -d $PWD/* | head -20` – Show the first 20 files with full pathnames - `du -sh *` – Show the size of all files and folders in the current directory (human-readable format) - `du -sh <folder_name>` – Display the size of a specific folder - `du -sh .` – Show the total size of the current directory - `du -sh * | sort -h` – Sort files and folders by size (smallest to largest) - `du -sh * | sort -hr | head -20` – Show the **20 largest files/folders** in the current directory - `ls -lhS | head -20` – Show the **20 largest files** in the current directory - `find . -type f -exec du -h {} + | sort -hr | head -20` – List the **20 largest files** recursively in current and subdirectories - `df -h` – Display disk space usage for all mounted file systems (human-readable format) - `df -h /path/to/dir` – Show available disk space for a specific directory path ### One-Liner: Counting Folders Missing Compressed Files A common HPC hygiene check — scanning a batch of result folders (e.g. GWAS summary statistics) for any that are missing their expected `.gz` output: ```bash count=0 for dir in sumstats_FG*/; do if ! ls "$dir"/*.gz >/dev/null 2>&1; then echo "No .gz file in: $dir" ((count++)) fi done echo "Total folders without .gz files: $count" ``` ## Basic Vim Commands - `vim <filename>` – Open a file in Vim (creates it if it doesn’t exist) - `i` – Switch to **Insert mode** (to start editing text) - `Esc` – Exit Insert mode and return to Normal mode - `:w` – Save (write) the file - `:q` – Quit Vim - `:wq` – Save and quit Vim - `:q!` – Quit without saving changes - `x` – Delete the character under the cursor - `dd` – Delete the current line - `yy` – Yank (copy) the current line - `p` – Paste the copied or deleted text below the cursor - `/pattern` – Search forward for a pattern in the file - `n` – Repeat the last search in the same direction - `u` – Undo the last action - `Ctrl + r` – Redo an undone action - `gg` – Go to the beginning of the file - `G` – Go to the end of the file ## Searching with `grep` - `grep "ACTG" <filename>` – Find lines containing ACTG - `grep -v "N" <filename>` – Exclude lines with "N" - `grep -c "rs" <filename>` – Count lines with "rs" - `grep -w "chr1" <filename>` – Match whole word "chr1" - `zgrep "chr1" <filename>.vcf.gz` – Grep inside gzipped VCF file ## Column Operations with `awk` - `awk '{print $1}' <filename>` – Print 1st column - `awk '$5 > 0.05' <filename>` – Filter rows with 5th column > 0.05 - `awk 'NR>1' <filename>` – Skip header (first row) - `awk 'BEGIN{FS="\t"} {print $2,$3}' <filename>` – Tab-delimited input ## Working with `.vcf.gz` Files - `zcat file.vcf.gz | head` *Shows the top lines including headers and first few variants* - `zcat file.vcf.gz | tail` *Shows the last few lines — useful for trailing info* - `zcat file.vcf.gz | grep '^#'` *Shows all header lines (metadata + column names)* - `zcat file.vcf.gz | grep -v '^#'` *Skips headers and shows actual variant records* - `zcat file.vcf.gz | grep -v '^#' | cut -f10 | head` *Displays the contents of the FORMAT/sample column* - `zcat file.vcf.gz | grep -v '^#' | wc -l` *Counts the number of data (variant) rows* - `zcat file.vcf.gz | grep -m1 '^#CHROM' | cut -f9` *Extracts FORMAT field labels (e.g., ES:SE:EP:AF:AFKG)* - `zcat file.vcf.gz | grep -v '^#' | awk 'NR <= 5 { print $3, $4, $5 }'` *Prints rsID, REF, and ALT for the first 5 variants* ## Finding Files with `find` - `find . -name "*.vcf"` – Find all .vcf files - `find /data -type f -size +1G` – Files >1GB in `/data` - `find . -mtime -1` – Modified in last 24 hrs - `find . -exec grep "rs123" {} \;` – Search "rs123" in all files - `find . -mindepth 1 -maxdepth 1 -type d | wc -l` - Count the number of folder inside a folder - `find . -name "filename.txt"` – Search for a file named **filename.txt** in the current directory and subdirectories - `find /path/to/search -name "filename.txt"` – Search for a file in a specific directory path - `find / -name "filename.txt" 2>/dev/null` – Search the entire system (suppress "Permission denied" errors) - `locate filename.txt` – Quickly search for a file using the system’s file index (requires `mlocate` or `plocate` installed) - `find . -iname "filename.txt"` – Case-insensitive search for the file name ## Text Processing Essentials - `cut -f1,3 <filename>` – Cut fields 1 and 3 - `sort <filename>` – Sort lines - `sort -k2,2n <filename>` – Sort by 2nd column numerically - `uniq -c <filename>` – Count unique lines - `paste <file1> <file2>` – Merge files side by side - `wc -l <filename>` – Count lines in a file ## Genomic Data Tools - `samtools view <file>.bam` – View alignment data - `bcftools view <file>.vcf.gz` – View VCF data - `bedtools intersect -a <a.bed> -b <b.bed>` – Genomic region overlap - `plink --bfile <data> --assoc` – Run basic association test ## Common HPC command - `srun --time=02:00:00 --mem=8G --cpus-per-task=2 --pty bash` – Start an interactive session on the HPC - `squeue` – View the job queue - `squeue -u <user_id>` – View jobs from a specific user - `squeue --help` – View additional options for `squeue` - `sacct -j <job_id>` – Get the status of a specific job - `scontrol show job <job_id>` – View extended information for a specific job - `seff <job_id>` – View running jobs with estimated CPU usage efficiency - `scancel <job_id>` – Cancel a specific job - `scancel -u <user_id>` – Cancel all running jobs for a user - `sinfo -N` – View the current load on the queuing system - `squeue --states=PENDING` – Show only pending jobs in the queue - `squeue -u <user_id> --states=PD` – Show only your pending jobs - `squeue | grep PD | wc -l` – Count how many jobs are pending system-wide - `squeue -u <user_id> | grep PD | wc -l` – Count how many of your jobs are pending --- ## Next Steps These commands cover the majority of day-to-day file inspection and job management, but a few directions are worth exploring next: writing small `awk`/`bash` scripts to automate recurring QC checks, learning `sbatch` for submitting batch (non-interactive) HPC jobs, and using `tmux` or `screen` to keep long-running sessions alive after disconnecting. ::: {.tag-row} [sbatch]{.tag} [tmux]{.tag} [Shell Scripting]{.tag} [QC Automation]{.tag} :::