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 _maskedQC.bgen.bgi _maskedQC.sample	soft link from /work
QC	gwas_siteQC	siteQC-filtered bgen v.1.2 files, 8-bit, ref-first siteQC-filtered pgen files	_filtered_final.bgen _filtered_final.bgen.bgi _filtered_final.sample	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 .results.txt .varianceRatio.txt	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 _qqplot.png _manhattan.png