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.