Code for creating and analyzing a genome-wide tandem repeat (TR) truth set based on publicly-available data from the Synthetic Diploid Benchmark [Li et al. 2018]

For more details, see:

Insights from a genome-wide truth set of tandem repeat variation Ben Weisburd, Grace Tiao, Heidi L. Rehm bioRxiv 2023.05.05.539588

---

Creating the truth set

After cloning this repo, see:

./run_all_steps.sh

This script runs all the steps for creating the truth set, launching downstream analyses, and generating the tables & figures for the paper.

---

Tool comparisons

Results from benchmarking widely-used STR callers using this truth set:

https://broadinstitute.github.io/str-truth-set/html/tool_comparison_viewer.html