Samtools is a command-line toolkit for inspecting and manipulating sequencing alignment files in SAM, BAM, and CRAM formats. Its common jobs include converting formats, sorting and indexing alignments, retrieving reads from a genomic region, collecting statistics, and checking files after transfer. This guide targets samtools 1.24, released July 9, 2026; command options may differ in other versions.
What samtools does—and what it does not do
Samtools provides tools for working with sequence alignments: it can convert, sort, merge, index, filter, retrieve, and report on alignment data. It is part of a related project ecosystem: HTSlib provides the underlying high-throughput sequencing format library, samtools provides alignment utilities, and bcftools handles variant calling and VCF/BCF data. The project describes the software as available under the permissive MIT licence. Samtools project overview
File-format semantics are specified through the GA4GH Large Scale Genomics work stream; samtools’ manual documents how this program behaves. For format questions, consult the GA4GH HTS specifications alongside the samtools manual.
Convert or inspect an alignment file with samtools view
samtools view can display alignments, filter them, select a genomic region, or write a different alignment format. By default, it outputs SAM text. Choose BAM or CRAM output with the relevant format option; for example, the commands below write BAM or CRAM, respectively:
Free tools Windows power users keep installed
One-click scans. No signup required.
#1 Best Overall
- Read Before You Buy — No Video Output: These adapters support charging and USB 2.0 data transfer, but cannot transmit video signals. Except for standard USB webcams (which use USB data only), they are not compatible with HDMI/DisplayPort cables, video-capable USB-C hubs, or docking stations with video output.
- Convert USB-A Ports to USB-C: Designed to connect USB-C earphones, cables, flash drives, card readers, and other USB-C accessories to standard USB-A ports. Plug-and-play with no drivers or software required.
- Aluminum Alloy Housing: Built with a sturdy aluminum alloy shell that aids in heat dissipation and protects against daily wear and scratches. Designed to maintain a stable and secure connection.
- Compact & Travel-Friendly: The ultra-compact design allows the adapter to stay plugged into your device without blocking adjacent ports or adding bulk, reducing wear and tear on your original USB ports.
- 12-Month Warranty: Backed by a 12-month manufacturer warranty for peace of mind. Designed to meet strict quality control standards for reliable everyday performance.
samtools view -b -o reads.bam reads.samsamtools view -C -o reads.cram reads.sam
To write SAM explicitly, use samtools view -o reads.sam reads.bam. Use samtools view -h reads.bam when you want the header included in displayed SAM output. Check the installed version’s help for available options and any reference requirements for your input and output formats.
Sort and index a BAM file for regional access
Random access to an alignment region requires a coordinate-sorted file and its index. Samtools sorts by leftmost coordinate by default; name sorting is a distinct mode. Sorting also updates the file header to indicate the sort order. Do not index a name-sorted file for coordinate-based region queries.
Rank #2
- 5-in-1 USB-C Hub: Experience comprehensive connectivity featuring a Power Delivery input, two USB-A 2.0 ports, a USB-A 3.0 port, and an HDMI port. (Note: The USB-C power delivery input port is only for connecting an external wall charger to power your laptop and cannot power peripheral devices.)
- 90W Pass-Through Charging: Achieve optimal charging with 90W pass-through power to your laptop, supported by a total input of 100W, with the hub reserving 10W for operational efficiency. (Note: Wall charger not included.)
- Quick Data Transfers: Accelerate your productivity with rapid data transfers using a high-speed 5Gbps USB 3.0 port and two 480Mbps USB 2.0 ports.
- 4K HDMI Display: Enhance your visual experience with a hub capable of delivering 4K resolution at 30Hz in both mirror and extend modes. Please note that this hub is compatible with MacBook (macOS 12 and newer), Windows 10 and 11, ChromeOS, and laptops equipped with DP Alt Mode and Power Delivery. Note: This device is not compatible with Linux.
- What You Get: Anker USB-C Hub (5-in-1, 4K HDMI), welcome guide, 18-month warranty, and our friendly customer service.
- Coordinate-sort the alignments:
samtools sort -o reads.sorted.bam reads.bam - Create the index:
samtools index reads.sorted.bam - Retrieve alignments overlapping a region:
samtools view reads.sorted.bam chr1:100000-101000
Replace chr1:100000-101000 with the reference name and 1-based region notation used by your data. The index enables samtools to seek to the region rather than read the entire alignment file. samtools view selects alignments overlapping the requested region; it is not a guarantee that each read is wholly contained within the interval. The manual also documents remote FTP and HTTP(S) access, including obtaining an index when needed if one is not available locally; regional retrieval depends on the server and index being accessible. samtools 1.24 manual
Index a FASTA reference and extract sequence
samtools faidx indexes a FASTA reference and can retrieve a requested reference subsequence. For an uncompressed FASTA, create its index and extract a region as follows:
Do these 3 things before closing this tab:
1Clear out junk files and repair common Windows errors2Fix the driver behind crashes, sound loss and screen glitches3Repair Windows errors before they cause bigger problemsRank #3
- Sleek 7-in-1 USB-C Hub: Features an HDMI port, two USB-A 3.0 ports, and a USB-C data port, each providing 5Gbps transfer speeds. It also includes a USB-C PD input port for charging up to 100W and dual SD and TF card slots, all in a compact design.
- Flawless 4K@60Hz Video with HDMI: Delivers exceptional clarity and smoothness with its 4K@60Hz HDMI port, making it ideal for high-definition presentations and entertainment. (Note: Only the HDMI port supports video projection; the USB-C port is for data transfer only.)
- Double Up on Efficiency: The two USB-A 3.0 ports and a USB-C port support a fast 5Gbps data rate, significantly boosting your transfer speeds and improving productivity.
- Fast and Reliable 85W Charging: Offers high-capacity, speedy charging for laptops up to 85W, so you spend less time tethered to an outlet and more time being productive.
- What You Get: Anker USB-C Hub (7-in-1), welcome guide, 18-month warranty, and our friendly customer service.
- Build the FASTA index:
samtools faidx reference.fa - Extract the requested subsequence:
samtools faidx reference.fa chr1:100000-101000
The compressed-reference case has a format requirement: the manual specifies BGZF-compressed input for compressed FASTA files. A generic gzip-compressed FASTA should not be treated as interchangeable with BGZF for this workflow. samtools manual
Mark duplicates with the required preparation
samtools markdup is not a one-command operation on arbitrary alignments. Its input must be coordinate-sorted and first prepared with name sorting and fixmate -m; fixmate supplies mate-related tags used by duplicate marking. One typical sequence is:
Rank #4
- Dual Converters, Infinite Potential：Includes 2× USB C male to USB A female adapters and 2× USB A male to USB C female adapters. Perfect for a wide range of uses—tablets with Bluetooth keyboards, expand USB ports on macbook, and more. Two different converters for all your daily needs
- Next-Level 10Gbps & 3A Charging: No more slow 480Mbps, this usb to usb c adapter has a transfer speed of up to 10Gbps, allowing you to do more transferring in less time. This usb adapter fits both USB A and USB C charger, supporting up to 3A fast charging
- Upgraded Exquisite Craftsmanship: With an aluminum alloy housing and metal connector, the usbc to usb adapter is extremely durable and sturdy. Rigorously tested to withstand more than 10,000 times of plugging and unplugging, ensuring long-lasting performance
- Broad Compatible: The usb c to usb adapter widely supports all USB C/ USB A devices like laptops, tablets, cellphones, car chargers, and phone chargers. Such as compatible with MacBook Pro/Air 2023/2022, Thunderbolt 4/3 Devices,Apple MagSafe Watch 9/8/7/SE/Ultra, iPad Pro 2022/2021, Samsung Galaxy S23/S20/S10, and iPhone 17/16/15 Pro. Plug and play
- Please Note: To reach 10Gbps speed, keep the cable under 3.3 ft. For USB A Male to USB C adapters, try flipping the USB C connector. USB C Male to USB A adapters support bidirectional 10Gbps transfer within 3.3 ft
- Name-sort:
samtools sort -n -o reads.name.bam reads.bam - Prepare mate information:
samtools fixmate -m reads.name.bam reads.fixmate.bam - Coordinate-sort:
samtools sort -o reads.coord.bam reads.fixmate.bam - Mark duplicates:
samtools markdup reads.coord.bam reads.markdup.bam
Use markdup only after these prerequisites are met, and consult the manual for options that match your input and intended duplicate-marking workflow. samtools manual
Check a transferred file without mistaking a quick check for a full scan
Run samtools quickcheck reads.bam for a fast preliminary check. It checks for a valid header and an intact end-of-file where applicable, but skips the middle of the file. A successful result therefore does not rule out internal corruption; use an appropriate full validation workflow when you need stronger assurance. samtools manual
What’s actually slowing this PC down?
Pick the symptom - the matching free tool is one click away.
Best Value
- 5-in-1 Connectivity: Equipped with a 4K HDMI port, a 5 Gbps USB-C data port, two 5 Gbps USB-A ports, and a USB C 100W PD-IN port. Note: The USB C 100W PD-IN port supports only charging and does not support data transfer devices such as headphones or speakers.
- Powerful Pass-Through Charging: Supports up to 85W pass-through charging so you can power up your laptop while you use the hub. Note: Pass-through charging requires a charger (not included). Note: To achieve full power for iPad, we recommend using a 45W wall charger.
- Transfer Files in Seconds: Move files to and from your laptop at speeds of up to 5 Gbps via the USB-C and USB-A data ports. Note: The USB C 5Gbps Data port does not support video output.
- HD Display: Connect to the HDMI port to stream or mirror content to an external monitor in resolutions of up to 4K@30Hz. Note: The USB-C ports do not support video output.
- What You Get: Anker 332 USB-C Hub (5-in-1), welcome guide, our worry-free 18-month warranty, and friendly customer service.
Choose the right command for the job
| Task | Command | Key condition |
|---|---|---|
| Convert or filter alignments | samtools view |
Specify the desired output format; regional queries require coordinate sort and index. |
| Order alignments | samtools sort |
Coordinate sort is the default; name sorting is a separate mode. |
| Enable random region access | samtools index |
Input alignment must be coordinate-sorted. |
| Index or extract from FASTA | samtools faidx |
Compressed FASTA input must be BGZF-compressed. |
| Mark duplicate alignments | samtools markdup |
Prepare with name sort and fixmate -m, then coordinate-sort. |
| Make a quick preliminary file check | samtools quickcheck |
Skips the file middle; it cannot detect internal corruption. |
Check your installed version’s command help
The official release list identifies samtools 1.24, dated July 9, 2026. Because commands and options can change, compare these examples with the manual for your installed version or run a command’s help before applying them to a production workflow. Official samtools releases
Quick Recap
Product prices and availability are accurate as of the date/time indicated and are subject to change. Any price and availability information displayed on Amazon at the time of purchase will apply.
