Up: Component summary
Up: Component summary
Component
PyCloneQCQuality checker for PyClone variant clustering tool. Work in progress. This tool supplants the PyClone analysis and requires PyClone version 0.13. For more information about PyClone, see https://bitbucket.org/aroth85/pyclone/wiki/Home and Roth et al., Nat Methods 11: 396, 2014.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Analysis |
| Authors | Antti Hakkinen (antti.e.hakkinen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | Python ; PyClone |
| Source files | component.xml launcher.py |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| config | YAML | Mandatory | PyClone configuration file |
| trace | BinaryFolder | Optional | PyClone trace directory (overrides that specified in the configuration file) |
| mutationFiles | Array<YAML> | Optional | Mutation files in the YAML format |
Outputs| Name | Type | Description |
|---|---|---|
| corr | CSV | Results of the correlation analysis of the traces |
| conv | CSV | Results of the convergence analysis of the traces |
| plots | BinaryFolder | Output directory for the plots |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| infCoverage | float | 1e100 | Variants with coverage no smaller than the specified will be considered as known, and will flaggedrto be excluded from the analysis. |
| plotType | string | "" | Comma separated list of the requested plot types. Options: "corr", "conv". |
| tolerance | float | 0.05 | Relative level of changes at which the correlations are assumed to be vanished and the series converged |
Test cases| Test case | Parameters▼ | IN config |
IN trace |
IN mutationFiles |
OUT corr |
OUT conv |
OUT plots |
|---|---|---|---|---|---|---|---|
| default | (missing) | config | trace | (missing) | corr | conv | (missing) |