Efficiently detect Structural Variant
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6 weeks ago
its.roops • 0

Dear All,

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?

variant Structural • 185 views
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how is it different from you previous question: Detect Structural varirant from VCF file ?

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It is more or less the same. But, I am looking for some efficient best performing tools that can detect if there is any SV in a very large VCF file typically containing millions of variants. Also, I am looking into programmatically detecting the same using Python efficiently as mentioned in the post.

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