Issues

• np.NAN in hatchet/utils/combine_counts.py

  raphael-group/hatchet#247 · Filter by author AaronHechmer opened on Aug 10, 2026

• plots display issue

  raphael-group/hatchet#238 · Filter by author tahashmi opened on Mar 17, 2025

• AssertionError [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?

  raphael-group/hatchet#232 · Filter by author immuneAI opened on Nov 6, 2024
  1

• HATCHet fails with new version of bcftools 1.21

  bug
  raphael-group/hatchet#227 · Filter by author simozacca opened on Oct 12, 2024
  8

  

• Using other reference genome builds

  raphael-group/hatchet#226 · Filter by author mhSepehri opened on Oct 6, 2024

• Incorrect CNV calculation of chrX and chrY

  raphael-group/hatchet#225 · Filter by author ywzhang071394 opened on Sep 23, 2024

• Issue runing Hatchet2 with hg38 reference_version

  raphael-group/hatchet#223 · Filter by author wchukwu opened on Jul 17, 2024
  5

• About "download_panel"

  raphael-group/hatchet#222 · Filter by author SuqinYang opened on Jun 26, 2024

• add flag and make GC correction optional

  raphael-group/hatchet#217 · Filter by author mmyers1 opened on Apr 18, 2024

• explore using more recent SHAPEIT version

  raphael-group/hatchet#214 · Filter by author mmyers1 opened on Apr 10, 2024

• resolve issue with CI testing python 3.7

  raphael-group/hatchet#213 · Filter by author mmyers1 opened on Apr 6, 2024

• HATCHet2 RDR/BAF locally-aware clustering error with sparse bins

  raphael-group/hatchet#206 · Filter by author aganezov opened on Feb 8, 2024

• can i ues this method for checking WGD of other species

  raphael-group/hatchet#205 · Filter by author WJT0925 opened on Jan 15, 2024

• Set default value for ILP time limit

  raphael-group/hatchet#204 · Filter by author mmyers1 opened on Jan 11, 2024

• Specifying size for WES samples in count-reads

  raphael-group/hatchet#199 · Filter by author bjlerman opened on Nov 20, 2023
  1

• Error when no reads are recorded in tumor.bed before/after centromere location

  raphael-group/hatchet#198 · Filter by author ronkesm opened on Nov 14, 2023
  2

• Error in plot_clusters() in plot_cn_1d2d.py due to change in pandas df.groupby()

  raphael-group/hatchet#197 · Filter by author BramLimSJ opened on Nov 2, 2023
  2

• Error in read_bb() in cluster_bins.py due to change in pandas df.groupby()

  raphael-group/hatchet#196 · Filter by author BramLimSJ opened on Oct 31, 2023
  4

• Full documentation is not in fact available from cs.brown.edu

  raphael-group/hatchet#195 · Filter by author ttriche opened on Oct 18, 2023
  3

• Failed to liftover chromosomes with picard

  raphael-group/hatchet#192 · Filter by author tahashmi opened on Jul 22, 2023

• Running HATCHet with phasing

  raphael-group/hatchet#191 · Filter by author um-pdavila opened on Jul 8, 2023

• Download 1000GP_Phase3

  raphael-group/hatchet#190 · Filter by author yqkiuo opened on Jun 9, 2023

• Falling at plot-bin step, even after adjusting -tR and -tB

  raphael-group/hatchet#189 · Filter by author immuneAI opened on Jun 2, 2023

• tabix parse error and cluster-bins failure

  raphael-group/hatchet#188 · Filter by author csmoreno opened on May 31, 2023
  4

• Phasing fails

  raphael-group/hatchet#187 · Filter by author csmoreno opened on May 3, 2023