SCORPI_GEL is a Java-based tool for processing genomic data using VCF files or catalogue (SBS) files to predict HRD, APOBEC, and MMRD, with built-in support for downloading and indexing reference genomes such as hg38.

Download and index reference genome FASTA files
java -jar -Xmx4g SCORPI_GEL_v2.jar Download {Genome_build} {path-to-download}

Example

java -jar -Xmx4g SCORPI_GEL_v2.jar Download hg38 /home/sunny/Sunnyveerla/Projects/ReferenceGenome/

Run SCORPI using a folder containing VCF files
java -jar -Xmx4g SCORPI_GEL_v2.jar VCF {path-to-ReferenceGenome} {path-to-VCF_folder} {FILTER (TRUE/FALSE)} {path-to-output_folder}

Example

java -jar -Xmx4g SCORPI_GEL_v2.jar VCF /home/sunny/Sunnyveerla/Projects/ReferenceGenome/hg38/hg38.fa /home/sunny/Sunnyveerla/Projects/SCORPI_GEL/Test/test_new/ TRUE /home/sunny/Sunnyveerla/Projects/SCORPI_GEL/Test/

Run SCORPI using a Catalogue (SBS) File
java -jar -Xmx4g SCORPI_GEL_v2.jar SBS {path-to-catalogue_file} {path-to-output_folder}

Example

java -jar -Xmx4g SCORPI_GEL_v2.jar SBS /home/sunny/Sunnyveerla/Projects/SCORPI_GEL/Test/rndm_2000snvs_r10_contextCountFile_complete_context.txt /home/sunny/Sunnyveerla/Projects/SCORPI_GEL/Test/