raphael-group/hatchet

Issues

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

  #232 opened 2 months ago by immuneAI
  0

• Incorrect CNV calculation of chrX and chrY

  #225 opened 4 months ago by ywzhang071394
  0

• Bioconda installs numpy >= 2.0 which is incompativle with HATCHet

  #229 opened 3 months ago by simozacca
  3

• Typo in the cluster_bin section of the hatchet.ini template file

  #231 opened 3 months ago by lconde-ucl
  0

• Issue running count-alleles from the demo-complete

  #228 opened 3 months ago by gaitat
  2

• HATCHet fails with new version of bcftools 1.21

  #227 opened 3 months ago by simozacca
  0

• Using other reference genome builds

  #226 opened 3 months ago by mhSepehri
  0

• 1KG panel for T2T version

  #224 opened 4 months ago by ywzhang071394
  1

• Issue runing Hatchet2 with hg38 reference_version

  #223 opened 6 months ago by wchukwu
  5

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

  #197 opened a year ago by BramLimSJ
  2

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

  #198 opened a year ago by ronkesm
  2

• About "download_panel"

  #222 opened 7 months ago by SuqinYang
  0

• Reference panel requirement

  #221 opened 7 months ago by willhooper
  1

• String "None" is not converted to Python `None` object in `parse_combine_counts_args`

  #208 opened 8 months ago by tyamaguchi-ucla
  0

• add flag and make GC correction optional

  #217 opened 9 months ago by mmyers1
  0

• AssertionError at clustering step

  #216 opened 9 months ago by willhooper
  1

• explore using more recent SHAPEIT version

  #214 opened 9 months ago by mmyers1
  0

• resolve issue with CI testing python 3.7

  #213 opened 9 months ago by mmyers1
  0

• Length of values does not match length of index

  #209 opened 10 months ago by tyamaguchi-ucla
  0

• Specifying size for WES samples in count-reads

  #199 opened a year ago by bjlerman
  1

• msr and mtr cannot be changed

  #185 opened 2 years ago by JenniferNeumaier
  1

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

  #206 opened a year ago by aganezov
  0

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

  #205 opened a year ago by WJT0925
  0

• Set default value for ILP time limit

  #204 opened a year ago by mmyers1
  0

• tabix parse error and cluster-bins failure

  #188 opened 2 years ago by csmoreno
  4

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

  #196 opened a year ago by BramLimSJ
  4

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

  #195 opened a year ago by ttriche
  3

• Failed to parse the output of the following command because the final objective was not found: {cmd}

  #193 opened a year ago by ronkesm
  2

• Failed to liftover chromosomes with picard

  #192 opened a year ago by tahashmi
  0

• Running HATCHet with phasing

  #191 opened 2 years ago by um-pdavila
  0

• Download 1000GP_Phase3

  #190 opened 2 years ago by yqkiuo
  0

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

  #189 opened 2 years ago by immuneAI
  0

• Phasing fails

  #187 opened 2 years ago by csmoreno
  0

• Convert count-reads output files to tabular format

  #186 opened 2 years ago by mmyers1
  0

• non-human genome

  #179 opened 2 years ago by gbnci
  1

• count() got an unexpected keyword argument 'stop'

  #184 opened 2 years ago by csmoreno
  0

• How can I download HATCHet v1.2.1 instead of v1.1.1?

  #183 opened 2 years ago by goldpm1
  0

• minK is not always enforced strictly for large K

  #182 opened 2 years ago by mmyers1
  0

• submitted in error

  #178 opened 2 years ago by mdiaz09
  0

• picard LiftoverVcf error

  #176 opened 2 years ago by zhujack
  0

• Sex chromosome plots

  #175 opened 2 years ago by miachom
  0

• ValueError: None potential neutral cluster found with given parameters!

  #174 opened 2 years ago by DecodeGenome
  2

• solver check FAILED after install Gurobi952

  #171 opened 2 years ago by DecodeGenome
  2

• the step "phase_snps" error

  #170 opened 2 years ago by DecodeGenome
  3

• Clean up visualization with many clones and many samples

  #173 opened 2 years ago by mmyers1
  0

• not support "run"

  #172 opened 2 years ago by gbnci
  0

• Error in installation

  #169 opened 2 years ago by jsha129
  0

• bulk.seg

  #168 opened 2 years ago by miachom
  0

• Building docker image on m1 macs

  #167 opened 2 years ago by shashkat
  0

• Error running combined-counts with phased SNPs

  #165 opened 2 years ago by wir963
  7