When running DeepVariant, the software may utilize a designated temporary directory, such as `/tmp/tmpcgn0s8jv`, to store intermediate files generated during the variant calling process. This directory serves as a workspace for holding data like aligned reads, assembled candidate variants, and other temporary outputs. The specific directory path, often randomly generated within the `/tmp` filesystem, ensures that these files are isolated and managed efficiently.
Storing intermediate files in a designated location offers several advantages. It facilitates efficient data management, as all intermediate outputs are consolidated within a single, easily accessible location. This streamlines the variant calling workflow and simplifies cleanup procedures after the analysis completes. Furthermore, utilizing the temporary filesystem (`/tmp`) leverages its inherent properties files stored within `/tmp` are typically removed upon system reboot, preventing accumulation of unnecessary data. This automated cleanup mechanism contributes to efficient disk space utilization and reduces the risk of cluttering the primary file system with temporary data. This practice also promotes reproducibility, as subsequent runs could potentially leverage cached data if available and properly configured.
