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. |
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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]]((https://github.com/Illumina/strelka)) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/strelka_somatic/strelka_somatic/)
is a module which corrects the sequences of structural variant calls (currently only insertions). [[Project link]](https://github.com/mkirsche/Iris) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/irissv/irissv/)
is tool is used to merge structural variants (SVs) across samples. [[Project link]](https://github.com/mkirsche/Jasmine) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/)
is probabilistic framework for structural variant discovery. [[Project link]](https://github.com/arq5x/lumpy-sv) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/lumpy_sv/lumpy_sv/)
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]](https://github.com/dellytools/delly) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/delly_call/delly_call/)
stands for Structural variant (SV) annotation and this is what is does. [[Project link]](https://github.com/dellytools/sansa) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/sansa_annotate/sansa_annotate/)
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]](https://github.com/fritzsedlazeck/Sniffles) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/)
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]](https://github.com/tjiangHIT/cuteSV) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/cutesv/cutesv/)
is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data. [[Project link]](http://boevalab.inf.ethz.ch/FREEC/) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/control_freec/control_freec)
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]](https://github.com/nanoporetech/medaka) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/)
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]](https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/)
is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format. [[Project link]](https://github.com/seqan/anise_basil) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/basil/basil/)
allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. [[Project link]](https://github.com/brentp/vcfanno) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/vcfanno/vcfanno/)
builds consensus sequence and call variants from amplicon-based nanopore sequence data. [[Project link]](https://github.com/artic-network/fieldbioinformatics) [[Galaxy tool]](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/artic_minion/artic_minion/)