Up: Component summary
Up: Component summary
Component
BICseq
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) |
| Issue tracker | View/Report issues |
| Requires | BICseq ; samtools ; THetA |
| Source files | component.xml BICseq.bash |
| Usage | Example with default values |
Inputs| 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 |
Outputs| 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. |
Parameters| 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 test |
IN control |
OUT results |
OUT calls |
OUT cloneCalls |
|---|---|---|---|---|---|---|
| case1 | properties | (missing) | (missing) | (missing) | (missing) | (missing) |
|
aligner=Bowtie, |
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