** Depreciated, check out GRIPper2: https://github.com/adamewing/GRIPper2 **

gripper README.txt

Adam Ewing <adam.ewing@gmail.com>

GRIPper is a tool to identify non-reference gene retrocopy insertion polymorphisms 
(GRIPs) from paired-end whole-genome sequence data, specifically tuned for Illumina 
reads.

Prerequisites:

bwa (http://bio-bwa.sourceforge.net/)
samtools (http://samtools.sourceforge.net/)
tabix (http://samtools.sourceforge.net/tabix.shtml)
pysam ( https://github.com/pysam-developers/pysam)
parallelpython (http://www.parallelpython.com/)

Usage:

There are a number of auxilliary files that specify details of the various
GRIPs one expects to find. Currently, gripper is configured to analyse human 
genomes; this can be changed by substituting the appropriate annotations for 
another species of interest.

* To begin, human_sample.cfg will have to be modified to assign
  'hg19' to a copy of hg19 that has been indexed by `bwa index -a stdsw`

* By default, GRIPper expects chromosome names to be prefixed by 'chr'. If this is
  not the case for your reference genome, use 'usechr' to 'False' in the config
  file (e.g. human_sample.cfg).

* To increase sensitivity, the parameter 'minPeakSize' may be decreased from the
  default of 8 reads to a minmum of 4 reads.

* If there is more than one sample (BAM file) specified in gripper.py, changing the
  -p command line flag will run multiple jobs in parallel.

Start by trying the included example (test/example.bam) with the following command:

./gripper.py -s samplelist_example.txt -c human_sample.cfg -o test

output will end up in test/example, the most relevant files are
uncategorized.tab.txt and uncategorizedbreaks.tab.txt, the former contains the 
coordinates and annotations, the latter contains breakpoint information.