Pooled parents paper

This repository contains code and analysis scripts for the pooled parents paper

Code in this repository

Summary of commands used

(including random seeds)

Command line scripts

filter_individualVCF.py filter_multiVCF.py

Pooled simulation pipelines

genotype_individuals.groovy pooled_sim_joint.groovy pooled_depth_joint.groovy freebayes.groovy freebayes_pool.groovy

Real pool and patients analysis pipelines

probands.groovy pooled_analysis.groovy

Analysis/plot scripts

pooled_paper_functions.R pooled_paper_simulation_plots.R

Data

Simons Simplex Collection samples

Melbourne Genomics Health Alliance samples

And the corresponding parent pool.