Detect Structural varirant from VCF file

Question

[its.roops]

Hi,

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.

[brunobsouzaa]

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!

Answer 1

[dthorbur]

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.

Answer 2

[Pierre Lindenbaum]

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