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The GWAS pipeline - detailed process output

Each process of the GWAS pipeline emits outputs that are directed to the child processes. Certain outputs are saved and copied to the final results folder.

Those outputs are:

Process group Process output subfolder suffix Output linkage Process function
QC gwas_maskingQC masked bgen v.1.2 files, 8-bit, ref-first gwas_bgen_siteQC _maskedQC.bgen
soft link from /work
QC gwas_siteQC siteQC-filtered bgen v.1.2 files, 8-bit, ref-first
siteQC-filtered pgen files
soft link from /work This process performs siteQC on the primary input files:
filters for maf and low missingness and performs a differential missingness test between cases and controls, and an HWE test on unrelated controls
SAIGE gwas_SAIGE_fit_null_glmm output from SAIGE step 1
Robject and text files containing the null fit
gwas_1_fit_null_glmm .rda
soft link from /work
SAIGE gwas_SAIGE_spa_tests_bgen per chunk/chr output from SAIGE step 2 (association tests) gwas_2_spa_tests .SAIGE.gwas.txt soft link from /work
GCTA gwas_GCTA_sparse_GRM sparse GRM files gwas_GCTA_sparse_GRM soft link from /work
GCTA gwas_GCTA_fit_null_glmm null GCTA fit gwas_GCTA_fit_null_glmm soft link from /work
GCTA gwas_GCTA_spa_tests_pgen per chunk/chr output from GCTA association tests gwas_GCTA_spa_tests .GCTA.gwas.txt soft link from /work
plotting plotting concatenated GWAS summaries manhattan and qqplot for GWAS plotting _summaries.txt