Recently 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.

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