Up: Component summary
Up: Component summary
Component
AscatRuns Allele specific copy number analysis with ploidy and tumor purity estimation using the tool ASCAT. A better description is available at the tool website
| Version | 1.3 |
|---|---|
| Bundle | microarray |
| Categories | Analysis |
| Authors | Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Source files | component.xml ascat.R AscatComp.R |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| tumorLogR | CSV | Mandatory | LogR file for tumor samples having the probe,chrs and pos in the first three columns, samples data in the rest (sample per column, probe per row) |
| tumorBAF | CSV | Mandatory | BAF file for tumor samples having the probe,chrs and pos in the first three columns, samples data in the rest (sample per column, probe per row) |
| controlLogR | CSV | Optional | LogR file for germline samples having the probe,chrs and pos in the first three columns, samples data in the rest (sample per column, probe per row) |
| controlBAF | CSV | Optional | BAF file for germline samples having the probe,chrs and pos in the first three columns, samples data in the rest (sample per column, probe per row) |
| gcContent | CSV | Optional | GC content file, if given, GC content normalization will be performed |
| gender | CSV | Optional | two columns csv file with the first column having sample names and second column having gender which can be "XX" or "XY". If not defined, all samples are assumed female "XX". |
Outputs| Name | Type | Description |
|---|---|---|
| results | BinaryFolder | A folder having one CSV file per sample containing the final segmentation. |
| summary | CSV | A file having a summary about ploidy and aberrand cell fractions estimated by ASCAT. Failed arrays will have NA values. |
| intermediate | BinaryFolder | A folder containing intermediate files produced by ASCAT. |
| plots | BinaryFolder | A folder containing plots produced by ASCAT. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| gamma | float | 0.55 | Platform related parameter. Available values are 0.55 for arrays and 1 for sequencing. |
| overrideHomoLimit | float | 0 | This option is used to override estimated HomoLimit parameter when a control sample is available. Default is 0 which means it will not override the estimated parameter. |
| penalty | int | 25 | Penalty of introducing more breakpoints during segmentation. It's not recommended to edit this parameter and modified value is only considered if one sample being analyzed. Default is 25. |
| platform | string | (no default) | The array platform. Supported values are "Affy100k", "Affy250k_sty", "Affy250k_nsp", "Affy500k", "Custom10k", "AffySNP6", "AffyOncoScan", "Illumina109k", "IlluminaCytoSNP", "Illumina610k", "Illumina660k", "Illumina700k", "Illumina1M" and "Illumina2.5M" |
| psi_manual | float | -1 | This parameter will override ascat optimization algorithm and provide a manual solution for psi, a ploidy related parameter. Can only be used when one sample is being analyzed. Negative values disable the option. |
| rho_manual | float | -1 | This parameter will override ascat optimization algorithm and provide a manual solution for aberrant cell fraction. Can only be used when one sample is being analyzed. Negative values disable the option. |
Test cases| Test case | Parameters▼ | IN tumorLogR |
IN tumorBAF |
IN controlLogR |
IN controlBAF |
IN gcContent |
IN gender |
OUT results |
OUT summary |
OUT intermediate |
OUT plots |
|---|---|---|---|---|---|---|---|---|---|---|---|
| case1 | properties | tumorLogR | tumorBAF | controlLogR | controlBAF | (missing) | gender | (missing) | (missing) | (missing) | (missing) |
|
platform=Custom10k |
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| case2 | properties | tumorLogR | tumorBAF | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) |
|
platform=Custom10k |
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