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Duplicate Alleles for the same position in output VCF #8

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caspargross opened this issue Jun 16, 2021 · 0 comments
Open

Duplicate Alleles for the same position in output VCF #8

caspargross opened this issue Jun 16, 2021 · 0 comments

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@caspargross
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IGV cannot read VCF Files produced by umiVar2 when there are two variants at the same position.

image

In the VCF files the problematic part looks like this:
image

Possible ways to solve this problem:

  • Only write one variant for each position
  • Postprocess the VCF file with bcftools norm -d to remove duplicates
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@caspargross