Introduction

SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

Pre-installtalation

Python Packages:

Scipy (http://scipy.org/)
Numpy (http://www.numpy.org/)
HTSeq (http://www-huber.embl.de/users/anders/HTSeq)

Running SVfinder

command-line usage

python SVfinder.py -i <input_mapped_reads.sam> -o <output.txt> [opts]

Options:

-n <int>    :cutoff of number of discordant pais to define a cluster  (default:2)
-l <int>    :extention length to join overlaped reads together (default:1000)
-r <int>    :read length (default:100)
-g <int>    :gene annotation file (default:hg19.ucsc.gene.txt)
-h          :produce this menu

Output

The output files include a output summary file and a output BED file. the discordant reads are listed in the folder with suffix '_svreads'.

A. The summary file consists of follwoing columns:

SV type (SVfinder support Insertion, Deletion, Inversion, Intra- and Inter-chromosome translocation)
of discordant read pairs
Chromosome 1
Position 1 start
Position 1 end
Orientation 1
Chromosome 2
Position 2 start
Position 2 end
Orientation 2
Annotation 1
Annotation 2
Putative gene fusion

B. The BED file consists of follwoing columns:

Chromesome
Position start
Position end
partener chr+start+end+strand
Orientation

cauyrd/SVfinder

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