It seems like Slice_bam should be pretty straight-forward to use, but when I run it and give it a bed file that contains the human chromosomes with their lengths like this:

chr1 1 249250621 chr2 1 243199373 for all chromosomes 1-22, X, Y.

I don't get the reads on chr1 and 2; instead, all I am left with are the reads on the nonstandard chromosomes (the unmapped scaffolds).

Any idea what I am doing wrong?

Jean Jasinski