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Incorrect VCF header formats #9

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

Incorrect VCF header formats #9

caspargross opened this issue Jun 16, 2021 · 0 comments

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@caspargross
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caspargross commented Jun 16, 2021 •
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VcfCheck and bcftools norm both show Issues with VCF File format:

  • Unsorted (enven for the *_sorted.vcf files)
  • Contig not defined in header
  • Filters not defined in header:
    • FDR
    • Low_Complexity
    • Low_AF
    • Strand_Imbalanced
    • Variant_Contamination
  • Info fields not defined
    • Variant_dist
    • Vicinity
  • Format ALT_COUNT not defined in header
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@caspargross