Arguments : bam1, bam2, RE_bed, outdir
The two input bam files represent two mates of the same sample and they're prepared by the first step of hictool.
The output files will go to the specified output directory as well. RE_bed is the bed file describing the restriction enzyme sites.
docker run -v /inputdir/:/data/:rw duplexa/hictool-bam2hdf5 run.sh /data/input.R1.bam /data/input.R2.bam /data/HindIII_hg19.bed /data/