Changelog

A quickreference summary detailing recent changes to the project.

Changelog

Table of contents

1. v1.0.2-ALPHA (2023-02-20)
   1. Features
2. v1.0.1-ALPHA (2023-02-07)
   1. Features

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v1.0.2-ALPHA (2023-02-20)

Features

Changes to ALL_COLLATE rule:

• Remove unnecessary variant renaming step. Variant renaming is now done during the LIFTOVER rule of the Vcf-Validation sub-pipeline only.

Changes to FILTER rule:

• Change filter stringency for samples and variants.

• Allow autosomal chromosomes only.

• Remove steps to filter out variants where the reference allele in the .vcf file does not match that of the reference genome. This step was unnecessary since variant reference alleles are altered to match that of the reference genome during the LIFTOVER rule of the Vcf-Validation sub-pipeline.

• Change variant nomenclature specifications for linkage-disequilibrium pruning step.

• Ensure that chromosome output is kept consistent by adding the --output-chr chr26 flag to all plink commands.

v1.0.1-ALPHA (2023-02-07)

Features

• Converted 20% missingness tests on variant and sample levels to 100% missingness.
• Included version v1.1.1-ALPHA of Vcf-Validation external pipeline.

Started tracking active changelog on 24 January 2023.