Process realigned BAM file to extract discordant human-virus reads
Proceeds in two steps:
Extract from BAMs all virus reads and human->virus paired-end discordant reads. Two files are created for each BAM:
virus_XXX.sam- has all reads which contain a virusdiscordant_XXX.sam- subset of above which has just reads which map to human whose mate maps to virus
This step can be time consuming, so support provided for cluster queuing system (bsub)
Note Due to TCGA restrictions we do not distribute the virus and discordant .sam files
Create BPC (breakpoint coordinates) file which lists human-virus discordant reads.
This is written to dat/BPC/XXX_Discordant.BPC.dat