Question

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

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4.3 years ago

BioinformaticsLad ▴ 200

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 • 1.9k views

ADD COMMENT • link updated 4.0 years ago by minalj365 • 0 • written 4.3 years ago by BioinformaticsLad ▴ 200

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

ADD REPLY • link 4.0 years ago by minalj365 • 0

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do you have a sample of the VCF being displayed?

ADD REPLY • link 3.9 years ago by cmdcolin ★ 3.8k

score 0 · Answer 1 · 2021-04-01

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.