CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

摘要： CNVnator 可用于基于个体基因组的read-depth（reads 深度）来发现CNV、和genotyping，还可以用于非常规的CNVs研究，如denovo（基于trio家系）和mutil-allelic。

CNVnator 运行中bin size选择：;100-bp bins for 20–30x coverage, ;500-bp bins for 4–6x coverage, and ;30-bp bins for 100x coverage。

-genotype 结果解读：

In the genotyping step, RD is normalized to 2 for chr1-22 and 1 for chrX,Y.

In your case (bin=100), you can estimate copy number as follows;

i) RD <0.5 ; homozygous deletion
ii) 0.5=< RD <1.5 ; heterozygous deletion
iii) RD>=1.5 ; Real copy number = round( normalized_RD by genotyping step )

Ex. chr22:1-10564800. normalized_RD=0.00501922 -> homozygous deletion (may be CN=0)
Ex2. chr22:10683901-10689000. normalized_RD=3.13349 -> real copy number = round(3.13349) =3