Licorice: This s GUI and command line tool to combine several VCF files in a single matrix. The CLI interface accepts one or more zip files with the vcfs, so you can download the zip directly from Torrent Suite and pass it directly to the software, you can also pass a directory with zips. The GUI only accepts one or more ZIP files. My original plan was to use GATK to merge all the VCF's, however it is too restrictive checking the VCF formating and it can fail with the files generated by TSVC, so I changed the vcf manipulation to bcftools, so I had to pack a precompiled version for linux and windows and it is in the ./licorice/native directory. The software supports few different output formats: One Column: The variants are in the A/B format Two Columns: A and B in different columns Non-Standadad: AB It can also output the results with SNPs in the columns and samples in the rows or transposed. Compile instructions git submodule update --init --recursive ./make_all.sh Execution: We have two executable jars, the command line inteface is compiled in: ./licorice/target/licorice-2.0-jar-with-dependencies.jar You can also run the CLI with the shell script ./licorice/licorice.sh The GUI is in: ./GUI/target/gui-2.0-jar-with-dependencies.jar Licorice: Licorice (alternatively spelled liquorice) comes from the root of a perennial plant native to a large swath of Eurasia. It takes nearly three years for a licorice root to be ready for harvesting, requiring several years of growth. It’s popular in its native regions as both a sweetener and component of natural medicine. It’s particularly of interest in gin, because the root itself is thought to have been widely used as a sweetening agent in early gins, including some Old Tom styles. Licorice has a distinctive flavor, similar to anise or fennel, but with a pronounced additional sweetness. It’s used in gins for both its flavor and for the sweetening effect.