Read in the structural variations predicted by SVseq2

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Description

Reading the structural variations predicted by SVseq2, filtering low quality predictions and merging overlapping predictions.

Usage

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    readSvseq(dataDir=".", regSizeLowerCutoff=100, method="SVseq2", 
              regSizeUpperCutoff=1000000, readsSupport=3) 

Arguments

dataDir

a directory containing the predictions of SVseq2.

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.

Details

The predicted SVs could be further filtered by the number of reads 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 SVseq2. The deletions output files should be named using the suffix ".del". See the example dataset for more details.

Value

A list with the following components:

del

the deletions predicted by SVseq2.

Author(s)

Wen Yao

Examples

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    svseq <- readSvseq(system.file("extdata/svseq2",package="intansv"))
    str(svseq)