HiNT36 was run with version: 2.2.7. hic_breakfinder38 was built from the master branch source downloaded from github, https://github.com/dixonlab/hic_breakfinder, using commit 30a0dcc6d01859797d7c263df7335fd2f52df7b8 (last updated in 2018). For hic_breakfinder the inter and intra chromosomal break files were provided by the Dixon lab as detailed on the github site. NextFlow pipelines to run both HiNT and hic_breakfinder can be found on the HiDENSEC github. EagleC37 was downloaded from https://github.com/XiaoTaoWang/EagleC and run with --prob-cutoff set to 0 so as to allow for calling of all possible variants. We were unable to install HiCTrans62 despite interactions with the authors due to deprecated dependencies of the hashmap R package.
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