intansv (version 1.10.0)

readDelly: Read in the structural variations predicted by DELLY

Description

Reading the structural variations predicted by DELLY, filtering low quality predictions and merging overlapping predictions.

Usage

readDelly(dataDir=".", regSizeLowerCutoff=100,  regSizeUpperCutoff=1000000, readsSupport=3, method="DELLY", pass=TRUE, minMappingQuality=30)

Arguments

dataDir

a directory containing the prediction results of DELLY.

regSizeLowerCutoff

the minimum size for a structural variation to be read.

regSizeUpperCutoff

the maximum size for a structural variation to be read.

readsSupport

the minimum read pair support for a structural variation to be read.

method

a tag to assign to the result of this function.

pass

set pass=TRUE to remove LowQual SVs reported by DELLY.

minMappingQuality

the minimum mapping quality for a SV to be read.

Value

A list with the following components:

del

the deletions predicted by DELLY.

dup

the duplications predicted by DELLY.

inv

the inversions predicted by DELLY.

Details

The predicted SVs could be further filtered by the number of read pairs supporting the occurence of a specific SV, and the predicted size of SVs to get more reliable SVs. See our paper for more details. The directory that specified by the parameter "dataDir" should only contain the predictions of DELLY. See the example dataset for more details.

Examples

    delly <- readDelly(system.file("extdata/delly",package="intansv"))
    str(delly)