A question about CNVnator resullt

Q:

Recently,I use CNVnator software detecting dog genome CNVs
using dog genome resequensing data from illumina GA platform.I have get the sorted and removed duplicated .bam file using bwa and samtools and then use command as follows to get CNVs result:

./cnvnator -genome Canis_familiaris.CanFam3.1.71.dna_rm.toplevel.fa -root GW2.root -tree GW2_sort.bam
./cnvnator -genome Canis_familiaris.CanFam3.1.71.dna_rm.toplevel.fa -root GW2.root -his 1000 -d genome_split/
./cnvnator -root GW2.root -stat 1000
./cnvnator -root GW2.root -partition 1000
./cnvnator -root GW2.root -call 1000 >GW2_result

I get result file(GW2_result),and then I convert it to VCF format using cnvnator2V! CF.pl,and get GW2_result_vcf file.I found the result is same what werid (I am new in genome CNVs analysis) because I find so many large-sizes duplications and indels in genome.I think the result file need same filter.But I do not know how to filter and do not find any filter information and standard by google,can you help me?Thank you very much!One of my results is in attachment,please check!

A:
thanks for interest to CNVnator.
Not sure what do you mean by many. How many?
Perhaps, some of those are gaps in the reference genome. While duplications are around those gaps.

Using CNVnator

Q:
CNVnator is a very popular software as observed though there is no official guide on CNVnator or any directions available on how to get started with CNVnator.Could you be kind enough to provide me with the same, please? Does your license allow to provide commercial services based on your program?

A:
Please download the software and read README file.

Alex Abyzov

Information in .root file

Q:
By using CNVnator, I managed to create the .root file but from there I can’t go any further because when I try to create the histograms, it seem to be working, but it never creates any files after it’s done.
A:
New information is added to the .root file you provided in the command line.
During next calculation step CNVnator will extract this information from the file.

To browse the content of the .root file you can start ROOT and open browser (type “new TBrowser”).

Please see http://root.cern.ch for details.

CNVnator license

Q:
Does your license allow to provide commercial services based on your program?

A:
Commercial services can use CNVnator for free provided that original software/developers/paper is credited/cited.

Alex Abyzov

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Department of Molecular Biophysics and Biochemistry,
Yale University, 260 Whitney ave., P.O. Box 208114,
New Haven, CT, 06520, USA
Phone: 1-(203)-432-5405
e-mail: abyzov@gersteinlab.org
URL: http://homes.gersteinlab.org/people/aabyzov
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