Having mapped the reads (paired-end) to a reference genome using BWA, I am trying to check the mapping results.
Using the tool "Summary Statistics" it supposed to be possible calculate the average insert size (ISIZE - column 9 from the SAM file).
However, the ISIZE column presents positive and negative values. Thus, the average value is always zero since the negative values cancel out the positive ones.
How can I deal with these negative values?