I am looking for some options to split a BAM file based on the insert size with the purpose of separating nucleosome free regions (i.e. regions below approx. 100bp) in ATAC-seq data from larger nucleosomal regions. As far as I can see from discussions at this site, some use deeptools/bamCoverage with specification of --maxFragmentLength to generate a bedgraph/bigwig file that only contains nucleosome free region. I would preferably like to keep the bam file format, so do any of you have some ideas to a commando/tool that do the job of splitting a bam file based on insert sizes.