Up: Component summary
Up: Component summary
Component
GenomicRearrangementCall genomic rearrangments. Four types of rearrangements can be found: duplications, deletions, inversions, translocations. You can read more about the parameters and inputs from the DELLY website.
| Version | 0.1 |
|---|---|
| Bundle | sequencing |
| Categories | CopyNumberAnalysis Short-read Sequencing |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | DELLY 0.0.10 or later ; installer (bash) |
| Source files | component.xml GenomicRearrangement.java |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| reference | AlignedReadSet | Optional | Input reference genome. Not setting reference will disable split-read analysis. |
| input | AlignedReadSet | Optional | Input BAM file for case sample. |
| folder | BinaryFolder | Optional | Folder of input files. |
Outputs| Name | Type | Description |
|---|---|---|
| delly | BinaryFolder |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| algorithm | string | (no default) | Type of rearrangement to call. There are four possible values: 'delly' for deletions; 'duppy' for duplications; 'invy' for inversions; and 'jumpy' for translocations. |
| dellyEnv | string | "../../lib/" | DELLY location in the system. By default the location is assumed to be globally defined by the environment variable '$DELLY_HOME'. |
| distMergeCutoff | int | 300 | Cutoff distance in bp for merging translocations. Only used if algorithm='jumpy'. |
| inversionOverlapMerge | int | 80 | Percentage of overlap to merge inversions. |
| madCutoff | int | 5 | Size of the insert-size cutoff. Only used if algorithm='delly'. |
| maxEpsilon | float | -1 | Maximum allowed deviation of PE vs. SR duplication. Negative values of this parameter use delly defaults. Only used if algorithm is one of 'delly', 'duppy', or 'invy'. |
| minFlankSize | int | 13 | Minimum length of the sequence flanking the putative breakpoint. |
| minMapQuality | int | 0 | Minimum mapping quality for a paired-end read. |
| verbose | boolean | false | Enable verbose output. |
Test cases| Test case | Parameters▼ | IN reference |
IN input |
IN folder |
OUT delly |
|
|---|---|---|---|---|---|---|
| case1 | properties | reference | (missing) | folder | (missing) | |
|
algorithm=delly, |
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| case2 | properties | reference | input | (missing) | (missing) | |
|
algorithm = invy, |
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| case3 | properties | (missing) | (missing) | folder | (missing) | |
|
algorithm = duppy, |
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