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Old 02-18-2018, 06:20 PM   #1
Seraphya
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Location: Melbourne Australia

Join Date: Oct 2013
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Default Recommendations for CNV calling algorithms/programs to benchmark

I want to benchmark the time/resource use and breakpoint accuracy of CNV callers on multiple individual NGS data at 30x-100x coverage at specific CNVs.

A few questions I have:

Is there a specific read mapper I should use to create the BAM file, or should I try a few for each SV/CNV caller?

Are there any specific algorithms/programs I should test? The only one I know I will test for sure is CNVnator as that is what has been used until now.

Anything else I should consider?
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cnv annotation, cnv calling, copy number analysis, structrual variation

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