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New and updated CNV and Variant Calling tools

on UseGalaxy.eu and in the Toolshed

Copy number variation (CNV) is a type of structural variation, specifically, it is a type of duplication or deletion events. During the last month, the Galaxy community has cooperated with the CNV community to bring a variety of the best CNV tools to the Galaxy ecosystem. In addition, we updated the variant calling tools, specifically to also cope with long read sequencing technologies. ELIXIR CNV community

In the following, you will find a list of a few highlights. We would like to thank all contributors, especially Nathan Roach, Niko Pinter, Stephan Flemming and the ELIXIR CNV community.


is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. Project link Galaxy tool


is a module which corrects the sequences of structural variant calls (currently only insertions). Project link Galaxy tool


is tool is used to merge structural variants (SVs) across samples. Project link Galaxy tool


is probabilistic framework for structural variant discovery. Project link Galaxy tool


is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. Project link Galaxy tool


stands for Structural variant (SV) annotation and this is what is does. Project link Galaxy tool


is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Project link Galaxy tool


is a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Project link Galaxy tool


is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data. Project link Galaxy tool


is a tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks applied a pileup of individual sequencing reads against a draft assembly. Project link Galaxy tool

GATK4 Mutect2

calls somatic short mutations via local assembly of haplotypes. Short mutations include single nucleotide (SNA) and insertion and deletion (indel) alterations. The caller uses a Bayesian somatic genotyping model. Project link Galaxy tool


is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format. Project link Galaxy tool


allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. Project link Galaxy tool

ARTIC minion

builds consensus sequence and call variants from amplicon-based nanopore sequence data. Project link Galaxy tool