Release notes - February 7, 2022
almost 3 years ago by Marko Marinkovic
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.