Automating the creation of IGV style histogram coverage maps

Question

[cxr5298]

Hello, I'm working on a pipeline using Bash, Python, and R to process metagenomic datasets. One of the features I want to incorporate is producing coverage maps for some hits depending on the read counts associated with them.

I know how to do this using IGV or UCSC genome browser and the necessary .bam and .bai files. However I want to automate this process so I won't need to manually do it each time. Some preliminary googling hasn't yielded much useful data. I was curious if anyone was aware of any Bash, Python, or R packages that have this same functionality?

Any help would be awesome, thanks!

Answer 1

[Pierre Lindenbaum]

I quickly wrote something like this using nextflow+ (samtools depth+R) a few weeks ago:

I imagine I should add another param to 'smooth' the curves.

It's CNV Tuesday. pic.twitter.com/0b2TebvZV8

— Pierre Lindenbaum (@yokofakun) June 4, 2019

Answer 2

[dariober]

If you are ok with R, have a look at Gviz. For something scriptable but with not very polished output see ASCIIGenome (disclaimer- I'm the author)