Margarita

Margarita infers genealogies from population genotype data and uses these to map disease loci.

These genealogies take the form of the Ancestral Recombination Graph (ARG). The ARG defines a genealogical tree for each locus, and as one moves along the chromosome the topologies of consecutive trees shift according to the impact of historical recombination events.

[Genome Research Limited]

Overview

Description

There are two stages to the analysis. First, we infer plausible ARGs using a heuristic algorithm, which can handle unphased and missing data. Second, we test the genealogical tree at each locus for a clustering of the disease cases beneath a branch. Since the true ARG is unknown, we average this analysis over an ensemble of inferred ARGs.

Publication

High resolution figures from the paper:

• Figure 1
• Figure 2
• Figure 3
• Figure 4
• Figure 5
• Figure 6

The method is described in:

• Mapping trait loci by use of inferred ancestral recombination graphs.

  Minichiello MJ and Durbin R

  American journal of human genetics 2006;79;5;910-22

  PUBMED: 17033967; PMC: 1698562; DOI: 10.1086/508901

Download

Margarita requires Java. See the documentation for further details.

FTP downloads

• Margarita
• Manual

Example input and output files

• Example 1 - A case-control study with phased sequences.
• Example 2 - The same case-control study as Example 1, but with unphased sequences.
• Output from running Margarita on Example 1.

Populations

• Margarita paper case-control studies

Links

Forward simulator for large genomic regions:

• http://www.ebi.ac.uk/projects/BARGEN
• http://www.ebi.ac.uk/projects/BARGEN/download/FREGEN/fregeneweb.html

Contacts

Questions about Margarita can be directed to Richard Durbin.