Issues

• 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

• Release vg v1.78.0

  vgteam/vg#5031 · Filter by author faithokamoto opened on Sep 9, 2026 · v1.78.0

• 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

• Help needed to understand the JSON output from a multimap aliment

  vgteam/vg#4995 · Filter by author MarionPerrier opened on Aug 3, 2026
  8

• 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

• Soft clipping with surject

  vgteam/vg#4892 · Filter by author schorlton-bugseq opened on May 2, 2026
  5

• Add a test for extremely long CIGARs in surject BAM output

  vgteam/vg#4890 · Filter by author adamnovak opened on Apr 28, 2026

• Remove logic we no longer need for handling GFA input specially

  vgteam/vg#4880 · Filter by author adamnovak opened on Apr 21, 2026

• How to find variant type when using vg deconstruct or vg call

  vgteam/vg#4874 · Filter by author ZhaoShuo0325 opened on Apr 11, 2026
  2

• Pruning with -u -M 32 still leads to GCSA indexing memory explosion (>1 TB) in spliced pantranscriptome graph

  vgteam/vg#4869 · Filter by author shin0727 opened on Apr 6, 2026
  1

• Different output between vg snarls and vg deconstruct -a

  vgteam/vg#4867 · Filter by author AliceLaurent opened on Apr 3, 2026
  4