Detect Structural varirant from VCF file
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4 months ago
its.roops • 0

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.

VCF Validation Structural Variants Validator • 396 views
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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!

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Entering edit mode
4 months ago
dthorbur ▴ 250

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.

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Entering edit mode
4 months ago

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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