vgteam/vg

Issues

• `vg call` strips path/contig info from vcf

  #4445 opened a month ago by CormacKinsella
  1

• Fail to deconstruct VCF from the GFA file generated by the PGGB pipeline and without erro report!

  #4444 opened a month ago by isaamael
  0

• Higher vg call AD values after using vg filter

  #4443 opened a month ago by danielwood1992
  0

• distance index slow to compute snarls

  #4420 opened 2 months ago by glennhickey
  3

• VG Paths --Metadata Warning: Duplicate Paths Exist in Graph

  #4440 opened 2 months ago by AbdelF6
  1

• Issue with vg call Generating VCF File for HBV Pangenome

  #4442 opened a month ago by lihuanhuan20000
  0

• does vg giraffe support the third mapping of precise long reads (PacBio HiFi, ONT) to graph-based pan-genomes?

  #4437 opened 2 months ago by ChenDepp
  1

• VG STATS: 2000 Properly Paired Inquiry

  #4434 opened 2 months ago by AbdelF6
  9

• Fix extremely slow read

  #4439 opened 2 months ago by adamnovak
  1

• Release vg v1.62.0

  #4435 opened 2 months ago by adamnovak
  0

• Release vg v1.61.0

  #4409 opened 3 months ago by adamnovak
  0

• Problem with vg inject in version 1.59

  #4415 opened 3 months ago by NMarthe
  0

• Demote Giraffe warnings that users can't fix to notices

  #4431 opened 2 months ago by adamnovak
  0

• Chromosome path not found in graph or haplotypes index

  #4411 opened 3 months ago by zwh82
  9

• Haplotypes in VCF not stored in xg index

  #4428 opened 2 months ago by rvarki
  4

• How to Generate a VCF File Showing Differences Between HG002 Haplotypes from the HPRC Pangenome

  #4419 opened 2 months ago by xuxingyubio
  4

• A question about vg filter.

  #4424 opened 2 months ago by pioneer-pi
  2

• Extracting specific path IDs for making subset gfa file

  #4423 opened 2 months ago by OZTaekOppa
  1

• Unrecoverable error in GCSA2 indexing

  #4406 opened 2 months ago by ld9866
  1

• Minimizer settings when using haplotype sampling

  #4418 opened 2 months ago by CormacKinsella
  6

• Reading GAM files in binary format directly

  #4416 opened 2 months ago by zhangyixing3
  5

• vg build fails on Apple M1 pro running Sequoia 15.0.1

  #4414 opened 3 months ago by dmgood11
  12

• sdsl-lite cmake issue

  #4389 opened 3 months ago by grenaud
  7

• Release vg v1.60.0

  #4374 opened 3 months ago by adamnovak
  2

• Giraffe alignment is very slow and produces warning[vg::Watchdog] messages unless rescue is disabled

  #4368 opened 5 months ago by polchan
  14

• Memory limit exceeded during vg autoindex for GCSA/LCP indexing

  #4404 opened 3 months ago by HuangXZhuo
  15

• Read coverage of haplotype sampling

  #4405 opened 3 months ago by SC-Duan
  2

• vg giraffe invalid alignment: Edit erroneously claims mismatch on node

  #4410 opened 3 months ago by ryandkuster
  2

• Negative or "*" end-position for named-coordinates gaf with giraffe

  #4386 opened 4 months ago by ASLeonard
  1

• Memory limit exceeded during vg autoindex for GCSA/LCP indexing

  #4403 opened 3 months ago by KANGYUlab
  0

• Error When Running "vg gbwt --gbz-format -g hprc-v1.0-mc-grch38.gfa.gz -G hprc-v1.0-mc-grch38.gfa"

  #4401 opened 3 months ago by AbdelF6
  1

• Issue Converting PGGB GFA Files for Panacus

  #4392 opened 3 months ago by OZTaekOppa
  4

• Update vg rna to project reasonably onto haplotypes containing CNVs

  #4399 opened 3 months ago by jeizenga
  0

• Hello, I have a question about vg map.

  #4398 opened 3 months ago by pioneer-pi
  1

• Throw an error "error: trying to access a snarl tree node of the wrong type" in `haplotypes`

  #4381 opened 4 months ago by wjwei-handsome
  11

• confused about the number of genome and gff files being provided to vg autoindex while mapping RNA data

  #4393 opened 4 months ago by QianghuiZhu
  3

• Hi, I have a question about vg augment.

  #4388 opened 3 months ago by pioneer-pi
  5

• Error when trying to map reads to a spliced-pangenome

  #4390 opened 3 months ago by CarlosAmadeo7
  8

• Different BAM alignments when using an Ubuntu 20.04 base image versus a 22.04 base image

  #4391 opened 4 months ago by dpuleri
  0

• The Amazing Uninjectable SAM

  #4379 opened 4 months ago by adamnovak
  1

• vg autoindex vg giraffe pggb gfa

  #4387 opened 4 months ago by hgz2021
  1

• Any option like BWA MEM '-C'?

  #4370 opened 5 months ago by alshai
  1

• Get input file error

  #4382 opened 4 months ago by OZTaekOppa
  5

• vg pack error

  #4384 opened 4 months ago by JONGHOLEE-myrrh
  0

• vg convert failes while converting gbz to xg with signal 6 error

  #4372 opened 4 months ago by leleory
  8

• `vg convert --vg-algorithm` loses start coordinates of paths in its W lines

  #4377 opened 4 months ago by zhangyixing3
  3

• Giraffe needs to better deal with systems where multiple processes opening the distance index causes slowdowns

  #4369 opened 5 months ago by adamnovak
  0

• How do different methods affect precision?

  #4366 opened 5 months ago by zhengluo-lz
  4

• vg call report missing allele

  #4358 opened 5 months ago by Han-Cao
  2

• vg call error

  #4360 opened 5 months ago by aaaniich
  2