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?
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?