Issues

• Broken link to documentation

  Wedge-lab/battenberg#177 · Filter by author MartinezRuiz-Carlos opened on Jun 2, 2026

• Incorrect PAR2 coordinates

  Wedge-lab/battenberg#176 · Filter by author wlippa opened on May 27, 2026

• LOH handling in prepare_wgs_cell_line.R

  Wedge-lab/battenberg#173 · Filter by author Mousiekin opened on May 1, 2026
  

• The tutorial 'https://wedge-lab.github.io/battenberg/' is invalid

  Wedge-lab/battenberg#171 · Filter by author LongpanICR opened on Mar 30, 2026

• Potential Issues in Current Development Version

  Wedge-lab/battenberg#163 · Filter by author HMU-WH opened on Oct 27, 2025

• Setting non-default parameters

  Wedge-lab/battenberg#162 · Filter by author davidwedge opened on Oct 22, 2025
  1

  

• chrX non-PAR only ?

  Wedge-lab/battenberg#161 · Filter by author panyuwen opened on Sep 5, 2025

• 'chr' removing added back and java version

  Wedge-lab/battenberg#160 · Filter by author Tim-Yu opened on Sep 1, 2025

• Using Battenberg outputs for GISTIC

  Wedge-lab/battenberg#159 · Filter by author ses101-24 opened on Jul 16, 2025

• Why Are BAFs Recalculated in Battenberg Instead of Using _Tumour_mutantBAF.tab

  Wedge-lab/battenberg#158 · Filter by author Mousiekin opened on Jun 12, 2025

• Suggestion: Add Support for Per-Chromosome Arm Imputation to Reduce Memory Usage

  Wedge-lab/battenberg#157 · Filter by author Mousiekin opened on Jun 12, 2025

• Does Battenberg support T2T-CHM13 genome?

  Wedge-lab/battenberg#156 · Filter by author DayTimeMouse opened on Jun 12, 2025

• Incorrect plotting of ChrX

  Wedge-lab/battenberg#153 · Filter by author jcesar101 opened on May 21, 2025
  

• odd conditional branch in filtcopynumber.R in pre_3.0

  Wedge-lab/battenberg#146 · Filter by author hidehitofukushima opened on Mar 1, 2025
  

• Problematic loci

  Wedge-lab/battenberg#142 · Filter by author Mousiekin opened on Jan 10, 2025

• Application of battenberg on long-read data

  Wedge-lab/battenberg#138 · Filter by author ywzhang071394 opened on Oct 6, 2024
  

• Copy number equals to 0

  Wedge-lab/battenberg#130 · Filter by author daisyyr opened on May 22, 2024
  2

  

• Incorrect TCS calculation in .vcf.gz file due to bug

  Wedge-lab/battenberg#126 · Filter by author tobyaicher opened on Jan 29, 2024
  

• Loss of previously called clonal events after callSubclones()

  Wedge-lab/battenberg#125 · Filter by author pblaney opened on Jan 15, 2024
  

• Error in if (tvar < 0) { : argument is of length zero

  Wedge-lab/battenberg#101 · Filter by author lydiayliu opened on Mar 31, 2023

• Multi-sample segmentation not saved

  Wedge-lab/battenberg#99 · Filter by author sdentro opened on Feb 21, 2023

• Is it possible to define either '%' or '# 'of clones and subclones

  Wedge-lab/battenberg#95 · Filter by author immuneAI opened on Oct 20, 2022
  1

  

• Missing homozygous deletion

  Wedge-lab/battenberg#88 · Filter by author seedgeorge opened on Aug 12, 2022
  1

  

• min_normal_depth used for tumour snps as well

  Wedge-lab/battenberg#87 · Filter by author seedgeorge opened on Jul 29, 2022