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). |