Genome In A Bottle Challenging Medically Relevant Genes Benchmark

This repository contains the code used to generate the figures and tables for Wagner et al.

Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes bioRxiv 2021.06.07.444885; doi: https://doi.org/10.1101/2021.06.07.444885

This analysis uses snakemake to preprocess input data for improved reproducibility and transparency and Rmarkdown files for manuscript figures and results.

Reproducing figures

The preprocessed figure input data files are included in this repository under data/tidy. To recreate the preprocessed data you will need to;

1. download files in the resource directory (see resource/README.md for file source),
2. run snakemake pipeline in the workflow directory,
3. regenerate figure input data files using analysis/00_tidying_data.Rmd, then
4. run individual scripts in analysis to create individual figure and tables.

Some figures were generate by manually modifying svg files exported from IGV. For transparency the IGV session files are included in analysis.

Repo Structure

Main repository directories include README.md files documenting code, data, or image files found in the directory.

.
├── analysis - code used to generate figures and tables
├── data - input data for figure code
├── data-raw - data from external analysis not documented in this repository
├── figures - figure image files
├── resources - input data file downloaded from external sources
├── scratch - work in progress analyses
└── workflow - snakemake pipeline home
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