After Next Gen Sequencing, alignment (BWA), sorting and indexing (samtools), I obtained a bam file. I would like to know there is any tool allowing me to , when using a sliding windows on a bam file, discriminate fragments fully spanning the window from the other ones ?
For instance : To calculate a score for a given window, i would add +1 for each fragment completely spanning the window and -1 for the fragments having an endpoint in the window. Any Suggestions please ?
Thanks in advance.