A collection of useful bioinformatics scripts I've written over time.
Description: Plot p-values vs. betas for a GWAS. Useful for identifying SNPs with low p-values and high betas. It uses Plotly to create an interactive plot.
Language: Python
Usage: see subdirectory README
Description: Take a sample file and shuffle the first two columns, so that the sample ID is first and the family ID is second. This is useful for Hail.
Language: Python
Usage: correct_sample_file.py <sample_file_name> <output_file_name>
Description: Take GEN files (e.g. IMPUTE2 output) and convert them to 8-bit sorted BGEN files organized by chr. Requires qctool.
Language: Bash
Usage: ./GENs_to_Sorted_8bit_BGENs.sh
NOTE: The script has a variable where the path to your GEN files should go. It should probably be an imput :/
Description: Take several summary statistics files and combine them into a single file suitable for a manhattan plot.
Language: Python
Usage: combine_manhattans.py <GWAS data directory> <project_prefix> <steps to run> <p-value threshold> <drop_repeats boolean>