INSTALLATION

From the FindTranslocation directory run

mkdir build
cd build
cmake ..
make

DESCRIPTION

FindTranslocations: tool to identify chromosomal rearrangements using Mate Pair or Pair End data. The idea is to identify areas having clusters of discordant pairs or abnormal coverage.

The SV module

The main FT modules, detects structural variant using discordant pairs, split reads and coverage information FindTransloctions --sv [Options] --bam inputfile

options:
ploidy - the ploidy of the organism, 2 is default
output - the prefix of the output files
    
max-insert - the maximum allowed insert size of a normal pair. Pairs having larger insert 
                than this is treated as discordant pairs. Default is 1.5*std+mean insert size for PE 
                data or 4std+ mean on mp data
                    
orientation - the pair orientation, use this setting to override the automatic orientation selection
        
pairs - the minimum number of discordant pairs used to all a variant. Default is 3
        
    q - the minimum mapping quality of the discordant pairs 
        forming a variant. Default value is 0.
                                    
    coverage - the library coverage. Default is calculated from average genomic coverage.

The cov module

Computes the coverge of different regions of the bam file FindTranslocations --cov [Mode] --bam inputfile

options:
bin - compute the coverage within bins of a specified size across the entire genome
        , outputs a tab file of the format chromosome    start  stop coverage
        
        
        light - compute the coverage within bins of a specified size across the 
                entire genome, outputs a tab file of the format chromosome  coverage

LICENCE

All the tools distributed with this package are distributed under GNU General Public License version 3.0 (GPLv3).