Genotype and merge VCFs from different samples

[Talo07]

Hi Dan,

I have 6 VCFs files per sample containing CNVs (each vcf file corresponds to one sample), issued from "CNVpytor". I want to genotype and merge my 6 VCFs files into a single VCFs file. On the other hand, for the SNVs I have a multisample VCF file (which includes all my samples).

I read README but I got confused between the merge of different caller of the same samples and same caller of different samples.

Could you please suggest the appropriate steps for my case ?

Thanks in advance :)