Getting started

The menu on the left lists several relevant topics for successfully running LDAK-KVIK. After downloading LDAK, it is possible to prepare your data using the input options. The command lines used to run LDAK-KVIK are included in the example code page. The example code page also includes command lines for generating fake genotype and phenotype data, and demonstrates how these can be used to run LDAK-KVIK.

A summary of the LDAK-KVIK algorithm is included in the steps of LDAK-KVIK, and the performance of LDAK-KVIK is showcased in performance page. It is possible to directly jump to a topic using search bar or the menu below. In case you have any questions regarding LDAK-KVIK or the LDAK software, please create an issue on the LDAK GitHub page.


Overview of LDAK-KVIK

Overview of LDAK-KVIK

Gene-based testing

Gene-based association analysis for genome-wide association studies

Single-SNP analysis

Single-SNP analysis

Saddlepoint approximation

Information about using the saddlepoint approximation in LDAK

Downloads

Getting started with LDAK-KVIK

Example code

Example code for running LDAK-KVIK

Input options

Overview of genotype, phenotype and covariate formatting options in LDAK-KVIK

LDAK-KVIK options

User options for running LDAK-KVIK

Output

Explanation of output files generated by LDAK-KVIK

Performance

Performance of LDAK-KVIK

Recommendations

Recommendations for running LDAK-KVIK

Technical details

Technical details of LDAK-KVIK

LDAK-KVIK on UKB-RAP

Running LDAK-KVIK on the UK Biobank Research Analysis Platform

Preparation

Preparing your data for using LDAK-KVIK on the UK Biobank Research Analysis Platform

Recommendations

Recommendations for using LDAK-KVIK on the UK Biobank Research Analysis Platform