Generates plink files for GRM - Githubissues

lifebit-ai / gwas

GWAS pipeline using SAIGE

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Generates plink files for GRM #114

Closed evagradovich closed 3 years ago

evagradovich commented 3 years ago

Overview

grm_plink_input parameter is now optional, creation of LD-pruned, genome-wide plink files is handled in the pipeline before SAIGE step
sampleFile parameter in SAIGE step and its hard-coded input is removed. It is not needed if vcfs are used as input for SAIGE >0.38 and we are using version 0.39.
parameterises phenotype column name - previously hard-coded to PHE

Test

Without --grm_plink_input:

https://cloudos.lifebit.ai/app/jobs/617c1efd2fc32701e672d61f

With --grm_plink_input for reproducibility of older jobs:

https://cloudos.lifebit.ai/app/jobs/617c1f142fc32701e672d8c4