Issues

• Release vg v1.79.0

  vgteam/vg#5071 · Filter by author parsaeskandar opened on Oct 19, 2026 · v1.79.0

• Improve sampled haplotype contiguity

  vgteam/vg#5070 · Filter by author jltsiren opened on Oct 19, 2026

• Take advantage of biological knowledge in haplotype sampling

  vgteam/vg#5069 · Filter by author jltsiren opened on Oct 19, 2026

• New .hapl version

  vgteam/vg#5068 · Filter by author jltsiren opened on Oct 19, 2026

• Haplotype Sampling Epic

  epic
  vgteam/vg#5067 · Filter by author jltsiren opened on Oct 19, 2026

• How to extract supporting read names for each genotyped SV site from vg call (v1.77.0)?

  vgteam/vg#5066 · Filter by author biozzq opened on Oct 18, 2026

• Usability Epic

  epic
  vgteam/vg#5065 · Filter by author adamnovak opened on Oct 16, 2026

• Putting generic paths in a GBZ into a reference sample is weirdly hard

  vgteam/vg#5064 · Filter by author adamnovak opened on Oct 16, 2026

• Genome Browser Intergration

  epic
  vgteam/vg#5043 · Filter by author parsaeskandar opened on Sep 21, 2026
  

• Remove vg viz

  epic
  vgteam/vg#5040 · Filter by author faithokamoto opened on Sep 17, 2026
  2

  

• Add a read-based likelihood mode to vg call

  Feature

  vgteam/vg#5037 · Filter by author adamnovak opened on Sep 15, 2026
  

• Genome Inference Epic

  epic
  vgteam/vg#5036 · Filter by author adamnovak opened on Sep 15, 2026
  1

• Pangenome Building Refinement Epic

  epic
  vgteam/vg#5035 · Filter by author adamnovak opened on Sep 15, 2026

• Purge .vg Epic

  epic
  vgteam/vg#5034 · Filter by author adamnovak opened on Sep 15, 2026

• Giraffe with extra threads is slower with a read-only distance index on a specific graph on a specific cluster

  vgteam/vg#5017 · Filter by author xchang1 opened on Aug 19, 2026
  4

• Retrieving haplotype/allele walks for a snarl

  vgteam/vg#5013 · Filter by author soum-stacks opened on Aug 18, 2026

• vg autoindex crashes with HPRC v2.0 GFA

  vgteam/vg#4971 · Filter by author BenTPTseng opened on Jul 20, 2026
  17

• vgci tests use randomized simulated reads, but this can make them fail spuriously

  vgteam/vg#4963 · Filter by author adamnovak opened on Jul 13, 2026
  2

• surject realigns a large portion of the read instead of splitting into supplementaries

  vgteam/vg#4959 · Filter by author faithokamoto opened on Jul 7, 2026
  6

• Get vg Debian package up to date

  vgteam/vg#4952 · Filter by author adamnovak opened on Jul 1, 2026

• mpmap can produce large negative mapping qualities, which are rejected by rpvg, and also rpvg can be very slow

  vgteam/vg#4944 · Filter by author caesarbulu opened on Jun 26, 2026
  5

• vg surject cannot produce properly-paired BAM for STITCH genotyping — is this fundamentally infeasible by design?

  vgteam/vg#4935 · Filter by author isaamael opened on Jun 16, 2026
  3

• Add a way to control where the explanation directories go from the command line

  vgteam/vg#4925 · Filter by author adamnovak opened on Jun 9, 2026

• People want to add tags to SAM read groups, and think they can be included in --read-group, but they can't

  vgteam/vg#4924 · Filter by author adamnovak opened on Jun 9, 2026

• Unexpected memory growth and empty output when mapping short RNA-seq reads to a pantranscriptome using mpmap

  vgteam/vg#4919 · Filter by author mt1022 opened on Jun 2, 2026
  6