I have a few VCF files (generated by unknown tools). Some of them contain short genetic variants while some contain structural variants. Is there any tool that can detect whether a particular VCF contains structural variants or not? Also, the tools need to be extremely efficient so that it can screen millions of variants that may be present in the VCF and report if there is any structural variant as per the definition from the VCF 4.3 specifications.
If there is no such tool, how can I detect SV using Python in a particular VCF file? I can understand that by scanning the header for certain keywords like SVLEN, SVTYPE, etc., this can be done. But what if there is no header and only the data fields? Is there any efficient way to detect a SV in a large VCF file?