From the FindTranslocation directory run
mkdir build
cd build
cmake ..
make
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 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.
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
All the tools distributed with this package are distributed under GNU General Public License version 3.0 (GPLv3).