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Table 1 Overview of CGTag tools available in NBIC/CTMM-TraIT Galaxy and the NBIC tool shed

From: CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy

Function Tool Description
Variant detection CGATools ListVariants Lists the non-redundant set of small variations found in an arbitrary number of genomes.
Variant detection CGATools TestVariants Determine which variants are found in which genomes given the results of ListVariants.
Variant detection CGATools CallDiff Compares two variant files to determine where and how the genomes differ.
Variant detection CGATools VarFilter Copies the input varfile or masterVar file, applying filters.
Variant detection CGATools JunctionDiff Reports difference between junction calls of CG junction files.
Variant detection CGATools Junctions2Events Groups and annotate related junctions.
Quality control CGATools SNPDiff Compares genotype calls to CG variant files.
File merge CGATools Join Merge two tab-delimited files based on equal field or overlapping regions.
Sequence retrieval CGATools DecodeCRR Retrieve sequences from a CRR file for a given range of a chromosome.
File conversion CGATools mkVCF Converts CG variant and/or junction files to VCF.
File conversion CGATools generateMasterVar Converts a varfile to a on-line-per-locus format.
File conversion CGATools fasta-2-crr Converts fasta sequences into a single reference crr file.
File conversion CGATools crr-2-fasta Converts crr file to fasta sequence.
File conversion TestVariants2VCF CG community tool. Converts output of the TestVariants tool to VCF.
Annotation ANNOVAR Functional annotation of genetic variants from high-throughput sequencing data.
Annotation MutationAssessor Functional impact of protein mutations.
Annotation Condel CONsensus DELeteriousness score of missense SNVs.
Visualisation CG Circos plots Create CG-style tumour, normal and somatic plots.
Visualisation Integrative plot Create circos plot from CG and SNParray data.
Visualisation Generic genomic data plotter Plot any type of numerical genomic data using GNUplot.
File manipulation Filter columns Filter tab-delimited files based on column contents.
File manipulation Add/remove chr prefix adds or removes chr prefix from chromosome column.
File manipulation Column select Extract and/or rearrange columns in tab-delimited file.
File manipulation Sort chromosomal position Sort a tab-delimited file by chromosomal position.
File manipulation Strip header Remove header from files.
File manipulation File concatenation Concatenate 2 files (e.g. for restoring header).