Oshlack / pooled-parents-paper

Code and analysis for the pooled parents paper

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.