{"title":"Release note 02.07.22","slug":"release-note-020722","body":"## Recently published apps\n\nWe have published 10 tools from the GRIDSS module software suite (toolkit) containing tools useful for the detection of genomic rearrangements:\n\n* **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.\n* **GRIDSS Extract Overlapping Fragments** is used to extract reads of interest for targeted GRIDSS variant calling.\n* **GRIDSS Annotate VCF Kraken2** adds Kraken2 classifications to single breakend and breakpoint inserted sequences.\n* **GRIDSS Annotate VCF RepeatMasker** adds RepeatMasker classifications to inserted sequences.\n* **GRIDSS GeneratePonBedpe** aggregates variants from multiple VCFs and counts the number of samples supporting each.\n* **GRIDSS SetupReference** is used for generating additional files for the reference needed for running GRIDSS.\n* **GRIDSS Somatic Filter** filters somatic calls from a VCF generated by GRIDSS joint tumor/normal variant calling.\n* **GRIDSS VIRUSBreakend** is a high-speed viral integration detection tool. It is designed to be incorporated in the WGS pipelines with minimal additional cost.\n* **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.\n* **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.","_id":"62012fc8ae2cee0380939c8d","changelog":[],"createdAt":"2022-02-07T14:42:16.242Z","user":{"name":"Marko Marinkovic","username":"","_id":"5767bc73bb15f40e00a28777"},"initVersion":{"version":"1.0","_id":"5773dcfc255e820e00e1cd50"},"project":"5773dcfc255e820e00e1cd4d","__v":0}

Release note 02.07.22


## 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.