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GenomicRearrangement

Call 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,
dellyEnv=../../lib/,
metadata.timeout=0

case2 properties reference input (missing) (missing)

algorithm = invy,
minMapQuality = 3,
verbose = false,
metadata.timeout=0

case3 properties (missing) (missing) folder (missing)

algorithm = duppy,
metadata.timeout=0


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