hicBuildMatrix supports the build of multicooler matrices, to do so, use as outfile format either .cool or .mcool and define for --binSize the desired resolutions. hicBuildMatrix builds the interaction matrix for the highest resolution and merges the bins to achieve the lower resolutions. The lower resolutions need to be an integer multiplicative of the highest resolution.
$ hicBuildMatrix -s forward.bam reverse.bam -o multi_resolution.cool
--binSize 10000 20000 50000 100000 --QCfolder QC