NewRecently published apps

We have published 10 tools from the GRIDSS module software suite (toolkit) containing tools useful for the detection of genomic rearrangements:

• GRIDSS tool, a structural variation caller for Illumina sequencing data. It calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.
• GRIDSS Extract Overlapping Fragments is used to extract reads of interest for targeted GRIDSS variant calling.
• GRIDSS Annotate VCF Kraken2 adds Kraken2 classifications to single breakend and breakpoint inserted sequences.
• GRIDSS Annotate VCF RepeatMasker adds RepeatMasker classifications to inserted sequences.
• GRIDSS GeneratePonBedpe aggregates variants from multiple VCFs and counts the number of samples supporting each.
• GRIDSS SetupReference is used for generating additional files for the reference needed for running GRIDSS.
• GRIDSS Somatic Filter filters somatic calls from a VCF generated by GRIDSS joint tumor/normal variant calling.
• GRIDSS VIRUSBreakend is a high-speed viral integration detection tool. It is designed to be incorporated in the WGS pipelines with minimal additional cost.
• GRIPSS applies a set of filtering and post processing steps on GRIDSS paired tumor-normal output. It produces a high confidence set of somatic SV for a tumor sample.
• GRIPSS Hard Filter applies a set of filtering and post processing steps on GRIDSS paired tumor-normal output. It produces a high confidence set of somatic SV for a tumor sample.

Marko Marinkovic