Protocol

The first three files provide step-by-step instructions for estimating SNP heritability, starting with raw genotype data. The final file provides tips for advanced analyses, including computing enrichment of a SNP set and estimating heritability when there are rare variants.

They are designed to be run as bash scripts on a UNIX operating system, but should also work in Terminal on a MAC (but are not suitable for Windows). The imputation guide requires a (phased) reference panel; we used 1000 Genomes Phase 3 (October 2014), which we downloaded from the IMPUTE2 website. A backslash (\) at the end of a line indicates a command spans multiple lines. Where mentioned, commands can be run in parallel; access to a cluster is highly recommended when performing imputation and when calculating SNP weightings for dense data.

Imputation of Cohorts

Merging Cohorts

Estimating SNP Heritability

Advanced Analysis

Weblinks:
PLINK | SHAPEIT | IMPUTE2 | Genome Browser
LiftOver which uses the files RsMergeArch.bcp.gz and SNPHistory.bcp.gz
Details of our imputation regions

If you spot any errors in the guides, please let me know!