Issues

• unused argument : min.cov in toil-vg vcfeval

  vgteam/toil-vg#835 · Filter by author zqfang opened on Jun 11, 2021
  2

• genotype calling for structral variants

  vgteam/toil-vg#834 · Filter by author zqfang opened on Jun 11, 2021
  4

• toil-vg construct fails at building the GBWT index if you haven't specially specified --vcf_phasing files

  vgteam/toil-vg#827 · Filter by author ruolin opened on Jan 1, 2021
  1

• Encoding issues with coordinates in id_ranges?

  vgteam/toil-vg#824 · Filter by author mlinderm opened on Aug 27, 2020
  1

• Make mkdir in dragen job fault tolerant

  vgteam/toil-vg#821 · Filter by author cmarkello opened on Aug 6, 2020
  

• Need better name for analysis subcommand

  vgteam/toil-vg#817 · Filter by author cmarkello opened on Jul 14, 2020
  1

  

• Merges to master time out in the CI tests

  vgteam/toil-vg#812 · Filter by author adamnovak opened on May 29, 2020

• run_whole_alignment doesn't output chromosomal BAMs

  vgteam/toil-vg#806 · Filter by author cmarkello opened on Apr 24, 2020
  4

  

• pip not python3 compatible

  vgteam/toil-vg#804 · Filter by author wharvey31 opened on Apr 21, 2020
  6

• --force_phasing True on toil-vg construct doesn't work

  vgteam/toil-vg#777 · Filter by author adamnovak opened on Dec 2, 2019
  2

• Flat requirements for whole genome mode are wasteful

  vgteam/toil-vg#773 · Filter by author adamnovak opened on Nov 15, 2019

• toil-vg call throws XGFormatError: Unimplemented XG format version: 0

  vgteam/toil-vg#759 · Filter by author alancleary opened on Aug 27, 2019
  4

• Pass variant names via the GBWT

  vgteam/toil-vg#741 · Filter by author glennhickey opened on Mar 27, 2019
  2

• toil-vg call takes over two days on yeast graph

  vgteam/toil-vg#737 · Filter by author eldariont opened on Mar 15, 2019
  12

• Support new surject options

  vgteam/toil-vg#736 · Filter by author glennhickey opened on Mar 13, 2019
  1

• Inversion logic timing out tests

  vgteam/toil-vg#724 · Filter by author glennhickey opened on Mar 1, 2019

• Test time dominated by R compiling stuff

  vgteam/toil-vg#723 · Filter by author glennhickey opened on Mar 1, 2019

• Multithreaded import doesn't work with S3 jobstore

  vgteam/toil-vg#703 · Filter by author glennhickey opened on Feb 1, 2019
  1

• Too many follow-ons which gbwt pruning with single vcf and many regions

  vgteam/toil-vg#700 · Filter by author glennhickey opened on Jan 30, 2019

• Support faster GBWT

  vgteam/toil-vg#670 · Filter by author glennhickey opened on Dec 17, 2018
  3

• Support ploidy in sveval

  vgteam/toil-vg#644 · Filter by author glennhickey opened on Nov 9, 2018

• 3rd test fails sporadically on Jenkins

  vgteam/toil-vg#641 · Filter by author glennhickey opened on Nov 7, 2018
  1

• toil-vg wastes time filtering down input VCFs when only asked for the --primary graph

  enhancementhelp wanted
  vgteam/toil-vg#610 · Filter by author adamnovak opened on Aug 20, 2018
  2

• Support Local Singularity Images

  vgteam/toil-vg#600 · Filter by author cmarkello opened on Aug 6, 2018
  

• Support GAM subsampling to mapeval on large read counts.

  vgteam/toil-vg#582 · Filter by author glennhickey opened on Jul 6, 2018
  1