1.20.c

samtools container

Main tool: samtools

Code repository: https://github.com/samtools/samtools

Additional tools:

• perl 5.34.0

Basic information on how to use this tool:

• executable: samtools
• help: --help
• version: --version
• description: Utilities for the Sequence Alignment/Map (SAM) format

Additional information:

This container includes samtools v1.20 compiled with libdeflate for a better cloud performance.

Full documentation: https://www.htslib.org/doc/samtools.html

Example Usage

samtools ampliconclip -b bed.file input.bam

samtools sort -T /tmp/aln.sorted -o aln.sorted.bam aln.bam