Can I use vg tools to calculate the depth for a bed range file like with samtools depth?

Question

[carolynzy]

Hi, I have some gam files produce by vg call and I want to know the mean/min/max depth for some ranges stored in a bed file. I could surject the gam file to the reference genome and convert to bam file, and then use samtools depth to calculate those statistics. However, maybe there is a way to do that with vg tools so that I don't need to do the convert steps?

Thanks for your help!

[carolynzy]

Thanks a lot! I will try these options immediately.

Answer 1

[glenn.hickey]

The closest thing to samtools depth is vg depth. vg depth doesn't accept bed files, but you can use it (with -k) to compute the coverage at each position in the whole chromosome (or genome) pretty quickly. Then you could pull out the intervals of interest with something like bedTools.

If you want to extract a bed region from your gam, you can use vg gamsort and vg chunk, but this will be much slower than depth. vg view cannot subset GAMs, so the above suggestion of using it will not work at all.

Answer 2

[Jordan M Eizenga]

Another option would be to use vg pack to compute node-level coverages in a .pack format and then use vg pack --as-table to print them out. There would be another layer of translation to get from a BED region to node IDs though.