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Nanopore structural variant calling - more than 2 alleles on IGV track?

I performed nanopore sequencing on human DNA and ran the Nanopore structural variant calling pipeline (miminmap2 + sniffles) against hg38. I loaded the VCF file into IGV and was surprised to see more than two alleles for most of my chromosomes (especially in the centeromeric regions). What does it mean to have > 2 alleles for a region? Is it simply a SV calling error? Or is a there a problem with the way IGV displays VCF tracks? Thanks!

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nanopore structural variant igv vcf
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updated by minalj365 • minalj365 • written by BioinformaticsLad BioinformaticsLad

Hi! Did you find answer? I get the same thing in IGV after minimap2 and sniffle. My data is PacBio

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written by minalj365 • minalj365

do you have a sample of the VCF being displayed?

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written by cmdcolin cmdcolin

1 answer

Hi all, for IGV questions please open issues at the IGV github site. (github.com/igvteam/igv/issues). I just ran across this while searching for something else. When posting include a sample VCF file. The display above does not show multiple alleles, rather multiple overlapping variants. This is not uncommon.

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written by Jim Robinson Jim Robinson

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