Genotyping

To genotype specific region one have to do the following

        ./cnvnator -root file.root -genotype bin_size [-ngc]

Once prompted enter a genomic region, e.g.

        >chr12:11396601-11436500

or

        >chr12 11396601 11436500

One can also perform instant visualization by adding word view, e.g.

        >chr12:11396601-11436500 view

or

        >chr12 11396601 11436500 view

For genotyping of large number of regions one can use input piping, e.g.

./cnvnator -root NA12878.root -genotype 100 << EOF
chr12:11396601-11436500
chr22:20999401-21300400
exit
EOF

For efficient calculations it is recommend you sort your list of regions by chromosome.