I wasn't able to find any clear documentation regarding this.
Does the CollectReadCounts tool count fragments (i.e. sets of paired-end reads) or individual reads over intervals? According to https://github.com/broadinstitute/gatk/pull/4564, this tool seems to have replaced CollectFragmentCounts which clearly stated it counts fragments according to this old documentation (https://gatk.broadinstitute.org/hc/en-us/articles/360036899412-CollectFragmentCounts-BETA-).
I assume that same functionality has been carried over into CollectReadCounts, but haven't found confirmation of this in the documentation or in the `--help` section. Also, if it does count fragments is there an option to get it to count individual reads?
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