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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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What level BAM should Lumpy be run on #332

Open icanwinwyz opened 4 years ago

icanwinwyz commented 4 years ago

Hello,

Can I run Lumpy on a GATK realigned and recalibrated BAM or in the original BWA mapped bam? Would the results vary drastically if we ran it on both?

Thanks!

ryanlayer commented 4 years ago

I am not sure. I have never tested this, but I would expect it to be okay.

On Sun, May 17, 2020 at 3:06 PM icanwinwyz notifications@github.com wrote:

Hello,

Can I run Lumpy on a GATK realigned and recalibrated BAM or in the original BWA mapped bam? Would the results vary drastically if we ran it on both?

Thanks!

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