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