Up: Component summary
Up: Component summary
Component
AnnToolsRuns one of the AnnTools variant annotator suite's scripts. Verify that anntoolsPath points to an AnnTools installation location. The MySQL server settings are read from the config.txt file in the AnnTools installation directory, so the user need not care about them once anntools has been deployed. The publication is available from AnnTools: A Comprehensive and Versatile Annotation Toolkit for Genomic Variants
| Version | 0.1 |
|---|---|
| Bundle | sequencing |
| Categories | External |
| Authors | Lauri Lyly (lauri.lyly@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | bash |
| Source files | component.xml main.bash |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| variants | TextFile | Mandatory | Variants in VCF or pileup format |
Outputs| Name | Type | Description |
|---|---|---|
| array | Array<VCF> | Output VCF files. |
| log | BinaryFolder | All other files. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| anntoolsPath | string | "/opt/anntools" | AnnTools installation path which needs to contain either run_cnv.sh, run_indel.sh or run_snp.sh, depending on the annotation mode. The standard installation has them. |
| format | string | "pileup" | Either pileup or vcf. Match your input file type. CNV may only accept VCF files. |
| mode | string | "snp" | One of snp, indel or cnv. CNV only accepts VCF files, otherwise you can choose. |
Test cases| Test case | Parameters▼ | IN variants |
OUT array |
OUT log |
||
|---|---|---|---|---|---|---|
| case_cnv | properties | variants | array | log | ||
|
format=vcf, |
||||||
| case_indel | properties | variants | array | log | ||
|
format=vcf, |
||||||
| case_snp | properties | variants | array | log | ||
|
format=pileup, |
||||||