How To Interpret The Numbers In The Cnvnator Genotype Output
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11.5 years ago
siyu ▴ 150

Using this CNV info, CNVnator does genotyping with -genotype option. Given the following command: ./cnvnator -root file.root -genotype 1000

chr1:102641001-102644000

CNVnator gave me the following output: Genotype chr1:102641001-102644000 file.root 3.26707 3.26707

Here are my questions.. Does anyone know what the last two values mean?

genotyping • 3.5k views
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Entering edit mode
13 months ago
lushjia • 0

CNVnator genotype output (*.genotype)

These files produced by CNVnator software. Each output file is space-separated text file, which consists of the following columns:
"Genotype" word
Chromosomic position like "chr1:99801-100600"
Source
Number of copies
Number of copies for low coverage samples

Example:
Genotype chrM:1-16600 5173T.root 576.984 563.799
Genotype chr1:1-13000 5173T.root 0.377524 0.368896
Genotype chr1:17601-51400 5173T.root 0.178211 0.174139
Genotype chr1:53301-54000 5173T.root 0.174089 0.170111
Genotype chr1:64201-64600 5173T.root 0.195805 0.19133

Here is where I got this information: http://wiki.biouml.org/index.php/CNVnator_genotype_output_(file_format)

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