discord-retro README.txt Adam Ewing <adam.ewing@gmail.com> discord-retro is a tool to identify transpoable element (TE) insertions from paired-end whole-genome sequence data, specifically tuned for Illumina reads. There are a number of auxilliary files that specify details of the various TEs one expects to find. Currently, discord-retro is configured to analyse human genomes; this can be changed by substituting the appropriate annotations for another species of interest. More details to come, but for now, users can try running discord-retro on the example .bam included (test/example.bam) with the following commandline: ./discord-retro.py -s samplelist_example.txt -c human_sample.cfg -o test/output in order for this to work, human_sample.cfg will have to be modified to assign 'hg19' to a copy of hg19 that has been indexed by `bwa index -a bwasw` output will end up in test/output/example, the most relevant files are other.tab.txt and otherbreaks.tab.txt, the former contains the coordinates and annotations, the latter contains breakpoint information. Prerequisites: bwa (http://bio-bwa.sourceforge.net/) samtools (http://samtools.sourceforge.net/) tabix (http://samtools.sourceforge.net/tabix.shtml) pysam (http://code.google.com/p/pysam/) parallelpython (http://www.parallelpython.com/)