This repositor contains a set of bash and python scripts used for GWAS analyses mostly based on plink.

If you are looking for scripts related to the Sweden exome dataset, you are mostly interested in the following master scripts:

install.sh
makegenes.sh
genovese2016.sh
genovese2016.R

Current version was updated on October 3rd 2016.

Basic script to convert text tables into XLSX tables (supports multiple sheets)

Identifies trios from a plink genome file and optionally generates PI_HAT x Z0 plot

Installs several resources useful for genetic analyses in a ~/res/ directory in your system

Perform basic quality control for markers in a plink dataset

Extracts a core set of highly confident non-rare 1000 Genomes project variants to analyze a given dataset befor marker QC

Compute several polygenic scores from either binary or dosage plink files and optionally adjusts them for covariates (e.g. principal components)

This scripts installs and generates several gene tables and lists useful for enrichment analyses

Performs basic quality control for samples in a plink dataset

Wrapper for performing burden analysis with SKAT (see https://www.hsph.harvard.edu/skat/) with several plink-like options

This script annotates a given VCF using the snpEff/SnpSift software and the dbNSFP database

This scripts converts VCF to plink following best practices (see https://bit.ly/1sgOcuP)