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:
chr11 249250621
chr21 243199373
for all chromosomes 1-22, X, Y.
I don't get the reads on chr1
I wanted to remove all the non-standard reads (reads from non-standard
chromosomes) from a bam file. I used Slice bam and the bed file contained all
of the chromosome lengths for chr1-22, x, and y. But all I get back in the bam
file are the unaligned chromosomes.
What am I doing wrong?
Jean
