Issues

• ERROR conda.core.link:_execute(730)

  bug
  mcvickerlab/varCA#47 · Filter by author xuanxuan-Jin opened on Jul 8, 2022
  1

• Exit (1) error when running pipeline using example data.

  bug
  mcvickerlab/varCA#46 · Filter by author rm1238 opened on Jun 23, 2022
  2

• add GT info to the VCFs

  enhancement
  mcvickerlab/varCA#43 · Filter by author shinlin77 opened on Apr 1, 2022 · VarCA v2.2.0
  11

  

• handling a scATAC custom reference genome from 10x

  documentation
  mcvickerlab/varCA#41 · Filter by author aryarm opened on Feb 19, 2022
  3

• Not all of the samples requested have provided input

  mcvickerlab/varCA#40 · Filter by author umasstr opened on Sep 9, 2021
  7

• warn or error gracefully if index files don't exist

  enhancement
  mcvickerlab/varCA#39 · Filter by author aryarm opened on Sep 3, 2021
  

• Error: "An output file is marked as pipe, but consuming jobs are part of conflicting groups."

  bug
  mcvickerlab/varCA#38 · Filter by author Rubbert opened on Aug 12, 2021 · VarCA v2.2.0
  12

  

• Single-end support

  enhancement
  mcvickerlab/varCA#37 · Filter by author Rubbert opened on Aug 4, 2021 · VarCA v2.2.0
  2

  

• comply with snakemake standards

  enhancement
  mcvickerlab/varCA#35 · Filter by author aryarm opened on Jul 14, 2021 · VarCA v2.2.0
  

• a smaller test dataset

  enhancement
  mcvickerlab/varCA#33 · Filter by author aryarm opened on Jul 4, 2021 · VarCA v2.2.0
  

• prepare.yml environment yields conflicts with strict channel_priority

  bug
  mcvickerlab/varCA#30 · Filter by author aryarm opened on Jun 26, 2021 · VarCA v2.2.0
  2

  

• Vardict error.

  duplicate
  mcvickerlab/varCA#24 · Filter by author lindenb opened on Mar 12, 2021
  2

• excessive memory usage when predicting variants

  bughelp wanted
  mcvickerlab/varCA#21 · Filter by author aryarm opened on Oct 26, 2020
  2

• ldpaths error when using prepare.yaml conda env

  bughelp wantedwontfix
  mcvickerlab/varCA#20 · Filter by author aryarm opened on Oct 23, 2020
  2

• only install the necessary variant caller dependencies

  breakingenhancement
  mcvickerlab/varCA#19 · Filter by author aryarm opened on Jul 15, 2020 · VarCA v2.2.0
  1

  

• snakemake validation

  breakingenhancementlow-priority
  mcvickerlab/varCA#18 · Filter by author aryarm opened on Jun 30, 2020 · VarCA v2.2.0
  1

  

• run the post-processing steps in the prepare pipeline in parallel

  enhancementlow-priority
  mcvickerlab/varCA#14 · Filter by author aryarm opened on Jun 9, 2020 · VarCA v2.2.0
  

• output figures in a snakemake report

  enhancementlow-priority
  mcvickerlab/varCA#7 · Filter by author aryarm opened on Jan 5, 2020

• don't use gatk selectvariants + allow varca to output SNVs and indels in the same VCF

  enhancementwontfix
  mcvickerlab/varCA#2 · Filter by author aryarm opened on Jul 15, 2019
  1