💾 Archived View for freeshell.de › tldr › samtools.gmi captured on 2023-07-10 at 14:55:40. Gemini links have been rewritten to link to archived content

-=-=-=-=-=-=-

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.

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

samtools view -S -b {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 - 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.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}

Copyright © 2014—present the tldr-pages team and contributors.

This work is licensed under the Creative Commons Attribution 4.0 International License (CC-BY).

CC-BY