This directory contains code used in the analysis of pathological microduplications described at https://rambutan.umassmed.edu/duplications/index.html

It includes several R scripts and the R Markdown file used to generate the webpage. Details are provided in the file headers and in comments throughout the code. A modified version of the function annotate_indels from the vt tool set (Tan et al., https://github.com/atks/vt) was also used; the modifications to the C++ source file annotate_indels.cpp are in the forked repository at https://github.com/oliverking/vt/tree/umms_branch

The analysis also relied on various publicly available datasets and software packages, not included here, as described on the webpage. 
Except where noted otherwise, code is Copyright (C) 2018, 2019 University of Massachusetts, licensed under the GNU General Public License v3.0; see LICENSE.txt file.

Please contact oliver.king@umassmed.edu if you have any questions.