1.17-2023-06

samtools container

Main tool:

• https://www.htslib.org/
• https://github.com/samtools/samtools

Additional tools:

• perl 5.34.0

Note about staphb/samtools:1.17-2023-06

This docker image is considerably smaller than the original staphb/samtools:1.17 docker image that was built using samtools/1.17/Dockerfile. Many unnecessary programs were removed and a builder stage was added for compiling & building the samtools executables. Programs such as python3 and gawk are no longer included in the final docker image.

If your workflows are failing, it may be because these programs were removed from the docker image to reduce the image size. We recommend using a different docker image (such as the docker image staphb/samtools:1.17!) if your pipeline requires the use of python3 or another program that was removed.

Example Usage

samtools ampliconclip -b bed.file input.bam

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

Better documentation can be found at https://www.htslib.org/doc/samtools.html