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Question: NGS alignment image drawing
0
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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

ADD COMMENTlink 4.0 years ago Raygozak ♦ 1.3k • updated 2.4 years ago h.mon 25k
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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?

ADD REPLYlink 4.0 years ago
John
12k
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Hi,

You can do this using Gviz R package.

ADD REPLYlink 2.4 years ago
tarek.mohamed
• 250
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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: https://www.biostars.org/p/158629/

ADD COMMENTlink 4.0 years ago Pierre Lindenbaum 120k
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Recently posted (hence my late answer): https://github.com/stevekm/IGV-snapshot-automator

ADD COMMENTlink 2.4 years ago h.mon 25k

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