v1.1.1

Changes

Documentation updated to reflect REGENIE as default mode for association testing, with SEAK deprecated.

v1.1

Breaking changes

• Makes gene_id_file mandatory in annotation config (resolves #158)

Other changes

• Saves an unfilled copy of the annotations so that NaN values can be modeled explicitly if desired
• make sure that every gene base exists once in gene id file (resolves #154)

Full Changelog: v1.0.4...v1.1

v1.0.4

• Clarify documentation for annotation pipeline
• Improvements to logging in snakemake pipelines

Full Changelog: v1.0.3...v1.0.4

v1.0.3

What's Changed

• Workaround for bug in bgen package that led to some missing genotypes

Full Changelog: v1.0.2...v1.0.3

v1.0.2

What's Changed

• Fixed a bug where SpliceAI_delta_score could be removed
• Fixed a bug in choice of validation samples
• Fixed conditiong window size (was 500kb not 500)
• Fixed Allelic Imbalance Filtering Logic for bcftools v1.16+
• Solved merge annotation attribute error
• Removed Anaconda defaults channel
• Skip seak association testing if all burdens are constant (SEAK erroneously gives a p-value of 0 if burdens are constant)

Full Changelog: v1.0.1...v1.0.2

v1.0.1

What's Changed

• Update testing config with deterministic flag by @meyerkm in #137
• Adding config creation features by @meyerkm in #138

Full Changelog: v1.0.0...v1.0.1

v1.0.0

First release version.

The results of the DeepRVAT publication can be reproduced using this version of the package.