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Ascat

Runs 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

case2 properties tumorLogR tumorBAF (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing)

platform=Custom10k


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