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Function: CNV CALLING
Usage: cnvnator -root file.root [-chrom name1 ...] -call bin_size [-ngc]
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Function: Visualizing specified regions.
Usage: cnvnator -root file.root [-chrom chr_name1 ...] -view bin_size [-ngc]
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Function: Calculating statistics for CNVnator. This step must be completed before proceeding to partitioning and CNV calling.
Usage: cnvnator -root file.root [-chrom name1 ...] -stat bin_size
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Function: RD signal partitioning
Usage: cnvnator -root file.root [-chrom name1 ...] -partition bin_size [-ngc]
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Function: Merging root files. Merging can be used when combining read mappings extracted from multiple files. Note, histogram generation, statistics calculation, signal partitioning, and CNV calling should be completed/redone after merging.
Usage: cnvnator [-genome name]-root out.root [-chrom name ...] -merge file1.root ...
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Function: Generating a histogram by using CNVnator
Usage: cnvnator [-genome name] -root file.root [-chrom name1 ...] -his bin_size [-d dir]
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Function: Genotyping genomic regions
Usage: cnvnator -root file.root -genotype bin_size [-ngc]