ExpansionHunterDenovo LRDN

A tool for local read depth normalization of ExpansionHunter denovo repeat expansion calls.

Requirements

There are several Python packages required to run the ehdn_lrdn.py and merge_lrdn_output.py scripts. These can easily be installed using pip and the requirements.txt file provided:

$ pip install -r requirements.txt

Usage

First, run the ehdn_lrdn.py script on each sample:

$ python ehdn_lrdn.py case_sample1.bam case_sample1 ehdn_output.tsv case_sample1.str_profile.json lrdn_output_dir/

After running the above script on all samples, run the merge script:

$ python merge_lrdn_output.py lrdn_output_dir/ lrdn_output.tsv