Output

After analysis, the final retained variants with annotations are stored in a compressed TSV format under the specified output folder. During the analyses, intermediate data for each task are stored in GTB format, facilitating efficient management of large datasets and enabling analysis resumption from specific breakpoints—a critical feature for studies involving extensive computational demands.

KGGA supports exporting processed genotype data to several commonly used formats, such as VCF and PLINK, to facilitate downstream analysis using other software tools.