is bedTools useful for this task?

[dnusol]

Hi,

I am not being able to select which tool from bedTools will do what I need, if any, but I am sure there must be one.

I have a positions file with two columns "chromosome" and "coordinate" and a coverage file with "chromosome" "coordinate" and "coverage".

Is there a tool for that?

Best,

D.

[mgogol]

If you mean that you want to go from a bed type file to a coverage type file, I think what you want is genomeCoverageBed or coverageBed, I can't really tell from your question. There is a pretty comprehensive manual.

And it sounds like you might need to modify your input first to include chromosome start and end coordinates.