jeltje/biobambam repository overview

See https://github.com/gt1/biobambam⁠ for details on biobambam

All tools are in /usr/local/bin

To run bamsort: docker run -v /my/local/data:/data jeltje/biobambam bamsort inputformat=sam level=1 inputthreads= outputthreads= calmdnm=1 calmdnmrecompindetonly=1 calmdnmreference=/data/ I=/data/<input.sam> O=data/<output.bam>

The reference must be samtools indexed (.fai). If you omit the I, input is expected to be STDIN, so you can pipe from e.g. bwa mem.