The tool is at: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html

I want to get base coverage for specific regions (I'll provide a bed file). However, the output is not in a standard BedGraph format that I can export into R for visualisation.

Q: How do I draw density plot of coverage over the regions from the outputs generated by the coverage tool?

Q: Alternatively, how to convert the non-standard outputs to a proper BedGraph? For example, the Sushi R package takes a bedgraph input file.
You should also consider bedtools genomecov, with the `-bg` option (bg being bedgraph)

http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html

Edit: After reading comments, and after some experimenting, what I think you want to do is:

```
bedtools intersect -a myBam.bam -b myRegions.bed > intersected.bam
bedtools genomecov -trackline -bg -ibam intersected.bam > intersected.bedgraph
```

Bedtools intersect will give only bam reads that overlap your regions (in myRegions.bed)

Then genomecov will draw a bedgraph file (coverage) only for the read depth for your filtered regions.