NGS alignment image drawing

Question

[Raygozak]

Hi, Does anyone know how can I draw programmatically a region of a bam alignment to a png image? I want to do this to examine several bam alignments at a time.

Thanks

[John]

Because this sounds a lot like what a genome browser does (IGV, USCS, etc) could you define what your png should look like that differs from a genome browser screen shot?

[tarek.mohamed]

Hi,

You can do this using Gviz R package.

Answer 1

[Pierre Lindenbaum]

You could control IGV over a port: https://www.broadinstitute.org/igv/PortCommands

I wrote a tool to convert a BAM to SVG: https://github.com/lindenb/jvarkit/wiki/Bam2SVG

See also: Alignment plot of a small extract (sequence) from a .bam file

Answer 2

[h.mon]

Recently posted (hence my late answer): https://github.com/stevekm/IGV-snapshot-automator