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The GWAS pipeline - Software versionsΒΆ

The pipeline is set up to run on the LSF cluster or AWS cloud.

As of 29 Sep 2022, the following software is used by the pipeline (v1.2) with the respective versions and usage:

Software Version Usage in pipeline
Nextflow 21.10.6 Workflow language
Bcftools 1.11-GCC-8.3.0 SiteQC directly on VCF files
Plink 1.9b_4.1-x86_64 Two steps of SiteQC on intermediate plink files:
1) Differential missingness filter.
2) HWE filter on controls.
Plink2 2.00-devel-20200409-x86_64 Format transformations between VCF/bgen/plink
bgenix 1.1.7 Indexing of bgen files
singularity 3.2.1 Running of all software via container images
SAIGE 1.0.7 Mixed model association analysis
GCTA 1.93.3beta2 Mixed model association analysis