I have several VCF files having structural variant. Is there any tool / tools that detect structural variants and automatically validate the vcf files if everything is in order as per the VCF format.
To search for structural variants you can use, for example, Manta or Pindel... Of course, there's a lot of other tools for that. To campare your VCF's you can easily do that using python or some tools like vcftools, for example!
Your question is unclear - what pipelines/tools were used to generate these SV VCFs and why wouldn't you trust them?
There are dozens of tools out there to detect SVs, reviewed here. You could then use a tool like SURVIVOR to merge VCFs from multiple tool and only accept overlapping SVs.
If your ambiguous question is about finding SV from a VCF file of small variants/SNVs, you can try bcftools roh https://samtools.github.io/bcftools/howtos/cnv-calling.html
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