McVean Lab

mccortex

De novo genome assembly and multisample variant calling

treeseq-inference

Work for the tree sequence inference paper.

TreeWAS

Corticall

Germline DNM caller based on LdBG assembly of pathogens

TreeWASDir

Repository for our manuscript 'Systematic classification of shared components of genetic risk for common human diseases'.

DEploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.

tskit-workshop

JupyterHub infrastructure for tskit workshops

DEploid-r

An R interface for dEploid. dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.

msprime

A reimplementation of Hudson's classical ms simulator for modern data sets.

schmidtWorkshop

Code used in Scmidt Science Fellowship workshop

bdiBeamer

mixedIBD-Supplement

Supplementary material for mixedIBD paper

PacBio

Assessments of PacBio datasets

PfDeconv

PfDeconv is now renamed as DEploid.

schmidtWorkshop-docker

Builds a docker image out of the schmidtWorkshop repo

stdpopsim

A library of standard simulation models for msprime