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Converting to VCF for SV breakpoints

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  • Converting to VCF for SV breakpoints


    Are there any well developed tools that convert SV breakpoints in bedpe or any other formats to VCF and properly generate BND / DEL / DUP format SVs?

    Options I have explored:

    svtools bedpetovcf: requires a very involved specific bedpe input, and generating this input would be more work than writing my own conversion to vcf

    breakpointGRangesToVCF: seems to have been removed from the StructuralVariantAnnotation package unfortunately

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