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Detects copy number alterations from whole-genome sequencing data using BICseq tool.

Version 1.0
Bundle sequencing
Categories Analysis
Authors Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI)
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Requires BICseq ; samtools ; THetA
Source files component.xml BICseq.bash
Usage Example with default values


Name Type Mandatory Description
test BAM Mandatory Input test sample in sorted and indexed BAM format
control BAM Mandatory Input control sample in sorted and indexed BAM format


Name Type Description
results BinaryFolder Folder containing all the output files produced by BICseq.
calls CSV CSV file for the final segmentation. The segments are classified into amplifications and deletions according to the threshold parameter. The original unfiltered segmentation file can be found in the folder output.
cloneCalls CSV Clone specific copy number by THetA algorithm. Only present if the parameter runTheta set to true.


Name Type Default Description
aligner string "BWA" The used aligner in the bam file inputs. BICseq accepts "BWA" or "Bowtie".
bicseqHome string "" The installation directory of BICseq.
binSize int 100 Initial bin size for BICseq.
chromosomes string "*" A set of comma-delimited chromosomes to be included in the analysis, "*" for all chromosomes included in the BAM inputs. The format should agree with the BAM files i.e. chr1 or 1.
insertSD string "500,50" Comma delimited insert size and standard deviation of the library.
lambda int 4 Lambda parameter affect the smootheness of the calls. recommended values 2 or 4, 4 for smoother profile.
outputName string "output" The base name for result files e.g. sample name.
pairedEnd boolean true Set true for paired-end reads.
runTHetA boolean false Whether to run ThetA to infer clone-specific copy number.
thetaDir string "" Path to ThetA bin directory.
threads int 2 Number of threads used when running ThetA
threshold float 0.25 Absolute value of the threshold for calling amplifications and deletions(negative).

Test cases

Test case Parameters IN
case1 properties (missing) (missing) (missing) (missing) (missing)


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