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I had the same problem and I haven't found any available tool to merge output from CNVnator...
I eventually used delly2 to find structural variants, because it handles multi-sample calling.
Sorry for replying to you so late. I just try delly2 and it seems to be very slow with command "delly call -t DEL -g $GENOME -o s1.bcf $BAM1 $BAM2 ......". So, I think I just can use "delly call -t DEL -g $GENOME -o s1.bcf $BAM1" separately and then merge them with "delly merge". Am I right?
Yes it's better to merge after, this is the pipeline I use (from the documentation on the github)
delly call on each bam :
delly call -t DEL -g your_genome.fa -o first_calling_1.bcf your_bam_1.bam
delly call -t DEL -g your_genome.fa -o first_calling_2.bcf your_bam_2.bam
merge all results :
delly merge -t DEL -o first_merge.bcf first_calling_1.bcf first_calling_2.bcf
re-genotyping on all detected positions :
delly/src/delly call -t DEL -g your_genome.fa -v first_merge.bcf -o second_calling_1.bcf your_bam_1.bam
delly/src/delly call -t DEL -g your_genome.fa -v first_merge.bcf -o second_calling_2.bcf your_bam_2.bam
merge with bcftools
bcftools merge -m id -O b -o final_merge.bcf second_calling_1.bcf second_calling_2.bcf
For the filters, I find that delly filter is too conservative, so I use my own filters (suppressing SVs with too much missing data, suppressing singletons...)
Thank you very much, especially for you are the first person who answer my question among my all questions! I'll try it.