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Add SamBamViz to pipeline #155

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niemasd opened this issue Jun 15, 2022 · 0 comments
Open

Add SamBamViz to pipeline #155

niemasd opened this issue Jun 15, 2022 · 0 comments

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@niemasd
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niemasd commented Jun 15, 2022

We've had a few occurrences in which stakeholders want to know how many reads had A, C, G, or T at each position of the genome, so I made a simple tool for performing interactive visualization of coverage:

https://github.com/niemasd/SamBamViz

I've been pulling trimmed BAMs and running SamBamViz manually on specific samples as requested, but given that it only takes ~3 minutes to run on a trimmed BAM to produce the TSV with base counts (which can be loaded up into the visualization web tool instantly), it would be great if it could be integrated into the pipeline so it's faster to view specific samples as requested

The current release is 0.0.8: https://github.com/niemasd/SamBamViz/releases/tag/0.0.8

Installation is easy (just a single script), and usage info can be found here:

https://github.com/niemasd/SamBamViz#usage

We would want to run it as follows, to reflect our cutoffs for iVar:

SamBamViz.py -q 20 -i TRIMMED_SORTED.BAM -o OUT_DIR
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