IMPUTE2: 1000 Genomes Imputation Cookbook

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Introduction

Authors

This page is based on a document prepared by Jian'an Luan, Alexander Teumer, Jing-Hua Zhao, Christian Fuchsberger and Cristen Willer for the GIANT Consortium.

Content

This page documents how to carry out imputation using IMPUTE2 software (developed by Jonathan Marchini and Bryan Howie) and 1000 Genomes reference panel haplotypes.

Before Imputation

Quality Control of Genotype Data

Before you start, you should apply appropriate quality control to your genotype data. This typically includes sample level quality control (examining call rate, heterozygosity, relatedness between genotyped individuals, and correspondence between sex chromosome genotypes and reported gender) and marker level quality control (examining call rates and deviations from Hardy-Weinberg Equilibrium and, for older genotyping platforms, excluding low frequency SNPs).

A good source of information on quality control checks for genomewide association data is:

Weale M (2010) Quality Control for Genome-Wide Association Studies. Methods Mol. Biol. 628:341–372 (in Barnes MB & Breen G (eds) Genetic Variation-Methods and Protocols, Chapter 19, Humana Press 2010) with code available from http://sites.google.com/site/mikeweale/software/gwascode

Convert Genotype Data to Build 37

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