Estimating percentage of overlap bewteen sam/bam/bed files

Question

[marioche]

Hi everyone,

I have 10 sam files and I want to estimate overall percentage of overlap between all the files. I saw the intersect option in bedtools and in bedops, but rather than having detailed information about the position and number of base pairs of overlap I prefer an overall percentage. Does anyone have an idea of how it can be done?

Thank you very much.

Marco

Answer 1

[Matteo Schiavinato]

But with bedtools you can also specify many different options, among which:

-wo            Write the original A and B entries plus the number of base pairs of overlap between 
               the two features. 
               Overlaps restricted by -f and -r. Only A features with overlap are reported.

From which you can then calculate the %.