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Commits on Sep 16, 2025

• Relocalisation of saige covariates in the config

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Commits on Sep 9, 2025

• Moved documentation from the Readme to the wiki

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• Changed name in default config file

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• Added flowchart image

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• Typos + publish xwas log

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• Added boolean for XWAS analysis

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• Renamed files and code to reflect the name change

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• Renamed HCL-GWAS to ARRAN in the readme

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Commits on Jul 23, 2025

• HWE can now "fail" silently

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Commits on Jul 21, 2025

• Added Standard Error to XWAS output

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Commits on Jun 25, 2025

• Added Summary Statistics

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• Booleans for steps + reorganisation of conf

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Commits on Jun 12, 2025

• Removed Sparse GRM + PCA on non-pruned set

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Commits on Jun 5, 2025

• Update Readme (started reorganisation and option description)

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Commits on May 28, 2025

• QQplot xwas + correction covar names

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• Added --xchr-model 2

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Commits on May 27, 2025

• Added XWAS association test

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Commits on May 26, 2025

• Modified the test dataset regions

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• Changed the test dataset + started chrX pipeline

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Commits on May 16, 2025

• new test dataset + correction CreateOutputRVAT

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Commits on May 15, 2025

• Sparse GRM + fix groupFile

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Commits on May 14, 2025

• Corrected split & regions

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Commits on May 7, 2025

• Files reorganisation

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• Added split between Autosomes and ChrX

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Commits on May 5, 2025

• Ajout paramètre "out_basename"

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Commits on Apr 9, 2025

• Ajout bed

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Commits on Apr 4, 2025

• Ajout jeu test

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• jeu test + ajouts PCs dans modele

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Commits on Feb 25, 2025

• Admixture + 'no-fail' + manhattan lines

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Commits on Feb 17, 2025

• Inclusion of Preprocess in QC wf + corrections

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Commits on Feb 13, 2025

• ReadMe update

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Commits on Feb 11, 2025

• start chrX genotypes + covariates offset

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Commits on Jan 31, 2025

• QQplot for rare variants + HWE threshold

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Commits on Jan 30, 2025

• Reorganisation plink files + HWE

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Commits on Jan 27, 2025

• Rscript for SAIGE groupFile

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