Issues

• invalid SNV confidence score

  vibansal/HapCUT2#144 · Filter by author Socrates1100 opened on Nov 21, 2025
  1

• Guidance on the use of error-corrected R10 ONT reads

  vibansal/HapCUT2#143 · Filter by author MoritzBlumer opened on Oct 2, 2025
  1

• --nf 1 clarification and the snakemake pipeline

  vibansal/HapCUT2#142 · Filter by author conchoecia opened on Aug 18, 2025
  2

• Incorrect phasing of variants in cis and trans orientation

  vibansal/HapCUT2#140 · Filter by author danchurova opened on Feb 21, 2025
  1

• Cram support

  vibansal/HapCUT2#139 · Filter by author JosephLalli opened on Feb 4, 2025
  1

• Indels phasing issue

  vibansal/HapCUT2#138 · Filter by author KonstantinTyurin opened on Nov 14, 2024
  2

• Release name for 1.3.3 tag wrong

  vibansal/HapCUT2#136 · Filter by author Flamefire opened on Apr 17, 2024
  1

• Core dumped

  vibansal/HapCUT2#135 · Filter by author seynard opened on Jan 29, 2024

• VCF with deletions

  vibansal/HapCUT2#134 · Filter by author dmjask opened on Nov 16, 2023

• HapCUT2 does not phase this variant directly adjacent to another and overlapping another other.

  vibansal/HapCUT2#132 · Filter by author jan-glx opened on Oct 26, 2023
  1

• Convert block file to vcf after pruning

  vibansal/HapCUT2#131 · Filter by author pdimens opened on Jul 25, 2023
  1

• Skip non-diploid or other invalid variants instead of raising error

  vibansal/HapCUT2#128 · Filter by author pontushojer opened on Jan 13, 2023

• Error while running extractHAIRS

  vibansal/HapCUT2#127 · Filter by author uncleflybfchen opened on Nov 16, 2022
  2

• calculate_haplotype_statistics.py slightly differs from block headers

  vibansal/HapCUT2#124 · Filter by author magnitov opened on May 4, 2022

• double free or corruption (out)

  vibansal/HapCUT2#121 · Filter by author tiffuhu opened on Nov 30, 2021
  1

• error while loading shared libraries: libhts.so.3

  vibansal/HapCUT2#120 · Filter by author sandipmkale opened on Nov 23, 2021
  1

• is this tool suitable for Creating a phased VCF of proximal variants?

  vibansal/HapCUT2#119 · Filter by author gudeqing opened on Oct 17, 2021
  1

• Is there a docker image for this tool?

  vibansal/HapCUT2#118 · Filter by author gudeqing opened on Sep 18, 2021
  2

• Segfault on extracthairs

  vibansal/HapCUT2#115 · Filter by author klannert opened on Jun 18, 2021
  2

• Obtaining Phased Haplotypes

  bug
  vibansal/HapCUT2#111 · Filter by author psur9757 opened on Mar 31, 2021
  5

• HapCutToVcf result deal

  vibansal/HapCUT2#109 · Filter by author LILIHAN-001 opened on Dec 28, 2020

• 10X Genomics data in hapCUT2

  vibansal/HapCUT2#90 · Filter by author burri-wildlight opened on Feb 6, 2020
  8

• extractHAIRS for polyploids

  vibansal/HapCUT2#82 · Filter by author sinamajidian opened on Sep 29, 2019
  1

• hapcut2 linkfragments error

  vibansal/HapCUT2#78 · Filter by author jakobcmueller opened on Jul 11, 2019

• UnicodeDecodeError during linked_fragment_file generation

  vibansal/HapCUT2#77 · Filter by author chunlinxiao opened on Jun 30, 2019
  27