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samtools — Tools for handling high-throughput sequencing (genomics) data. Used for reading/writing/editing/inde

Submitted by: @import:tldr-pages·Mar 2, 2026·

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Problem

How to use the samtools command: Tools for handling high-throughput sequencing (genomics) data. Used for reading/writing/editing/indexing/viewing of data in SAM/BAM/CRAM format. More information: <https://www.htslib.org/doc/samtools.html>.

Solution

samtools — Tools for handling high-throughput sequencing (genomics) data. Used for reading/writing/editing/indexing/viewing of data in SAM/BAM/CRAM format. More information: <https://www.htslib.org/doc/samtools.html>.

Convert a SAM input file to BAM stream and save to file:

samtools view -S {{[-b|--bam]}} {{input.sam}} > {{output.bam}}

Take input from stdin (-) and print the SAM header and any reads overlapping a specific region to stdout:

{{other_command}} | samtools view {{[-h|--with-header]}} - chromosome:start-end

Sort file and save to BAM (the output format is automatically determined from the output file's extension):

samtools sort {{input}} {{[-o|--output]}} {{output.bam}}

Index a sorted BAM file (creates sorted_input.bam.bai):

samtools index {{sorted_input.bam}}

Print alignment statistics about a file:

samtools flagstat {{sorted_input}}

Count alignments to each index (chromosome/contig):

samtools idxstats {{sorted_indexed_input}}

Merge multiple files:

samtools merge {{output}} {{input1 input2 ...}}

Split input file according to read groups:

samtools split {{merged_input}}

Code Snippets

Convert a SAM input file to BAM stream and save to file

samtools view -S {{[-b|--bam]}} {{input.sam}} > {{output.bam}}

Take input from `stdin` (-) and print the SAM header and any reads overlapping a specific region to `stdout`

{{other_command}} | samtools view {{[-h|--with-header]}} - chromosome:start-end

Sort file and save to BAM (the output format is automatically determined from the output file's extension)

samtools sort {{input}} {{[-o|--output]}} {{output.bam}}

Index a sorted BAM file (creates `sorted_input.bam.bai`)

samtools index {{sorted_input.bam}}

Print alignment statistics about a file

samtools flagstat {{sorted_input}}

Context

tldr-pages: common/samtools

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