Interpreting Bedtools Intersection Between BAM and BED Files

Question

[Steven Mick]

Hi,

I'm doing a bedtools intersection between a BAM and BED file and am getting a few columns of output that I don't know how to interpret. Running bedtools intersect -a <BAM> -b <BED> -bed -wo yields lines like the following:

chr1    12554   12654   rname_val   0   +   12554   12654   0,0,0   1   100,    0,  chr1    12613   12721   bed_name_val    0   +   41 

I believe I understand all but the following middle columns

12554   12654   0,0,0   1   100,    0,  

It appears to output the aligned read's coordinates and length, but I'm not sure what the other numbers are meant to signify. This particular output appears contingent on passing a BAM, as converting the BAM to BED and then running bedtools intersect -a <BAM converted to BED> -b <BED> -bed -wo yields the same row but without the central columns:

chr1    12554   12654   rname_val   0   +   chr1    12613   12721   bed_name_val    0   +   41

Any help would be appreciated! Thanks!