Output

Outputs at a glance

KGGSum operates using a task-by-task model. Each task generates efficient intermediate files (including binary variants*.gtb outputs) that store harmonized variants, statistics, and annotations. This design lets you resume interrupted workflows or re-run with new parameters without repeating completed steps (you can also branch workflows).

Option	Description	Default
--output	Specify the output folder path. All data from each task will be stored under this folder, preserving intermediate files and helping you avoid duplicate work. Format: --output <dir> Example: --output ./out/test	./kggsum
--clean-intermediate-data	Remove intermediate data to reduce disk usage and memory pressure. Format: --clean-intermediate-data	[OFF]

While each analysis has its own tasks, some common task outputs are listed below.

File	Description
ConvertVCF2GTBTask*.gtb	The gtb format file converted from the input VCF file by --ref-gty-file
GenerateRootVariantSetTask/variants.annot.hg38.gtb	The variants extracted from the reference genotype file specified by --ref-gty-file in gtb format will be used as the base for the following analysis.
AppendVariants2RootVariantSetTask/variants.annot.hg38.gtb	The base variants appended with GWAS summary statistics specified by the --sum-file
GeneFeatureAnnotationTask/variants.annot.hg38.gtb	The variants annotated with gene features subsequently
OutputVariants2TSVTask/variants.hg38.tsv.gz	The GWAS summary and annotations of variants retained for analysis in TSV format.