Issues

• refactor the package

  Bioconductor/VariantAnnotation#115 · Filter by author vjcitn opened on Jul 7, 2026
  4

• what is the "covr" condition of this package?

  Bioconductor/VariantAnnotation#114 · Filter by author vjcitn opened on Jul 7, 2026
  

• produce false positive and false negative PRs

  Bioconductor/VariantAnnotation#113 · Filter by author vjcitn opened on Jul 7, 2026
  2

• possible problem parsing INFO description field

  Bioconductor/VariantAnnotation#89 · Filter by author vjcitn opened on May 22, 2025

• ensemblVEP::parseCSQToGRanges

  Bioconductor/VariantAnnotation#88 · Filter by author peterjuv opened on Mar 7, 2025
  2

• locateVariants failing on intronic variants

  Bioconductor/VariantAnnotation#87 · Filter by author jayoung opened on Aug 9, 2024
  1

• expand() and non-standard rowRanges columns

  Bioconductor/VariantAnnotation#85 · Filter by author jayoung opened on Jul 19, 2024
  1

• nonsense mutations from DBS across two codons misclassified as nonsynonymous?

  Bioconductor/VariantAnnotation#84 · Filter by author ChristofferFlensburg opened on Jul 11, 2024

• Incorrect annotation of exon/intron boundary deletion

  Bioconductor/VariantAnnotation#83 · Filter by author mschubert opened on Jul 3, 2024

• readVcf does not recognize my vcf file?

  Bioconductor/VariantAnnotation#82 · Filter by author igrabski opened on May 15, 2024
  6

• locateVariants() and predictCoding() silently drop large INDELs

  Bioconductor/VariantAnnotation#81 · Filter by author johnstonmj opened on Apr 25, 2024
  5

• readVcf doesn't handle quoted = in hapmap_exome_chr22.vcf.gz correctly

  Bioconductor/VariantAnnotation#80 · Filter by author LTLA opened on Jan 2, 2024
  10

• Convert Number=A to Number=1 when creating an ExpandedVCF

  Bioconductor/VariantAnnotation#79 · Filter by author LTLA opened on Jan 2, 2024
  5

• Faithfully recapitulate metadata via a round-trip through writeVcf + readVcf.

  Bioconductor/VariantAnnotation#78 · Filter by author LTLA opened on Jan 2, 2024
  5

• readVcf(), VariantAnnotation and shiny compatibility

  Bioconductor/VariantAnnotation#77 · Filter by author FunGeST opened on Dec 8, 2023
  1

• expand Error data is NULL

  Bioconductor/VariantAnnotation#72 · Filter by author DarioS opened on Aug 13, 2023

• readVcf is Slow if ScanVcfParam which Regions is Lengthy

  Bioconductor/VariantAnnotation#70 · Filter by author DarioS opened on Mar 27, 2023
  4

• writeVcf Output Causes IGV Errors from htsjdk

  Bioconductor/VariantAnnotation#65 · Filter by author DarioS opened on Sep 12, 2022
  5

• Populate INFO column with VariantAnnotation::writeVcf

  Bioconductor/VariantAnnotation#61 · Filter by author Al-Murphy opened on May 31, 2022
  4

• locateVariants returns genes from both Forward and Reverse strands in PRECEDEID and FOLLOWID

  Bioconductor/VariantAnnotation#55 · Filter by author amizeranschi opened on Feb 23, 2022
  3

• readVcfStack(param=ScanVcfParam()) doesn't work if "which=" is not specified.

  Bioconductor/VariantAnnotation#50 · Filter by author Liubuntu opened on Oct 6, 2021
  1

• Can geno() obtain the reference depth and alternate allele separately?

  Bioconductor/VariantAnnotation#48 · Filter by author lihe-s opened on Sep 17, 2021
  1

• predictcoding - multiple mutations at a codon are never evaluated additively

  Bioconductor/VariantAnnotation#46 · Filter by author ojcharles opened on Mar 8, 2021
  1

• REFCODON not consistent with REF

  Bioconductor/VariantAnnotation#43 · Filter by author onebeingmay opened on Nov 3, 2020
  1

• Proposal: String representation/RleMatrix

  Bioconductor/VariantAnnotation#38 · Filter by author jonocarroll opened on Feb 28, 2020
  6