Necessary python modules: argparse pandas numpy peddy math
Install dependencies using conda:
conda env create environment.yml
conda activate strling-denovo
Utilizing STRling output as input, code now counts amplifications over bp threshold and determines Mendelian status (matched to parents, violation, etc.) at a certain depth threshold.
Command line might look something like:
python strling-MV.py --outliers STRs.tsv --ped file.ped --out output.tsv --wiggle 0.3 --minwig 10 --ampsize 100 --depth 12
pytest tests/test_strling-denovo.py