I'm trying to understand how the preprocessing of the mappability is implemented.
In the CopyhelpeR package the mappability is defined as followed:
"The mappability data were obtained by aligning all possible 51 base pair
genomic fragments using BWA (http://bio-bwa.sourceforge.net/). The
mappability of every fragment was binarized, and the mappability of a specific region
is taken as the average mappability of all fragments that fall into this region."
Now I'm wondering what the mappability of a fragment exactly is since
there is no such value defined in the SAM-Format and why you chose a bp length of 51.