Bedtools genomecov option to keep columns 4-6?

Question

[rioualen]

Hi, I'm using bedtools genomecov in order to get the coverage from one bedfile either with option -d (coverage per position) or -bga (bedgraph output). However my input bedfile comes in 6-column format, and the last 3 are not reported in the output files. I'd be particularly interested in keeping the score column, is there some option to do that? Thank you.

input.bed

NC_000913.3     91      5009       -      82.302  +
NC_000913.3     274     307        -      88.889  -
NC_000913.3     5320    5437       -      77.311  +
NC_000913.3     5551    5600       -      84.314  +
NC_000913.3     5556    5600       -      86.957  +
NC_000913.3     5565    5603       -      90.244  +
NC_000913.3     5565    5600       -      89.189  -

bedtools genomecov -d -i input.bed -g coli.genome

NC_000913.3     1       0
NC_000913.3     2       0
NC_000913.3     3       0
NC_000913.3     4       0
NC_000913.3     5       0
NC_000913.3     6       0

bedtools genomecov -bga -i input.bed -g coli.genome

NC_000913.3     0       91      0
NC_000913.3     91      274     1
NC_000913.3     274     307     2
NC_000913.3     307     5009    1
NC_000913.3     5009    5320    0

[zunyilim]

Hi, Did you ever figure this issue out? I'm having the same issue with my normalization with my spike-in using genomecov. It writes over my 4th column and deletes column 5 and 6 in my bed files, of which column 6 is my strand information which is important.

Thanks!