Welcome to LDAK-KVIK!

LDAK-KVIK is a tool for mixed-model association analysis for genome-wide association studies (GWAS). It is part of the LDAK software, which is written in C. A preprint of LDAK-KVIK is now online.

Key Features of LDAK-KVIK:

  • High efficiency: Capable of analysing 100,000s of individuals within hours
  • High statistical power: Improved detection of associated loci using an elastic net model
  • Structured data: Robust analysis of data with high levels of relatedness or multiple ancestries
  • Saddlepoint approximation: Control of type 1 error when testing rare diseases or variants
  • Gene-based association analysis: Leverage summary statistics in a gene-based association test

To download LDAK, please visit our downloads page. Example code of LDAK-KVIK can be found on the example code page. An overview of the steps involved in the LDAK-KVIK algorithm is included on the LDAK-KVIK steps page.

Stay updated with the latest developments regarding LDAK software by signing up for the LDAK mailing list.

Example code

LDAK-KVIK is run in three steps:

  1. Compute PRS using an Elastic Net model
  2. Run single-SNP analysis with PRS as an offset
  3. Conduct gene-based analysis using summary statistics from the single-SNP analysis

Example command lines are:

./ldak6.linux --kvik-step1 kvik --bfile data --pheno phenofile --covar covfile --max-threads 4
./ldak6.linux --kvik-step2 kvik --bfile data --pheno phenofile --covar covfile --max-threads 4
./ldak6.linux --kvik-step3 kvik --bfile data --genefile genefile --max-threads 4

The main output files are:

  • kvik.step2.assoc (results from single-SNP association analysis)
  • kvik.step3.remls.all (results from gene-based association analysis)

Installation

LDAK is compatible with both Linux and Mac. On the Downloads page, we list several options for loading or installing the LDAK software.

Questions or issues

For any questions or issues about LDAK-KVIK or the LDAK software, please Raise an Issue.