From NGS paired sequences and mapped onto a reference genome, SVDetect allows you to detect clusters of anomanously mapped pairs (with abnormal order, strand orientation or insert size of fragments), and to predict structural variants (SVs) such as large insertions, deletions, inversions, duplications or intra/inter-chromosomal translocations. SVDetect can also compare the results of SVs from different samples and to identify specific-sample SVs (Tumoral DNA vs Control DNA, for example).
SVDetect is compatible with any type of paired reads ("paired-end" or "mate-pair"), sequencing technology (Illumina, SOLiD, PGM, ...), or type of genome.
SVDetect can compute coverage profiles and to reveal loss or gains of genomic regions from the copy-number information.
It is available into a PERL Script and takes the BAM format as input.
SVDetect is also available at the Galaxy toolshed.