hartwigmedical/hmftools

Issues

• Building Cuppa

  #608 opened 18 days ago by weewus
  2

• Linx visualiser error

  #565 opened a month ago by mich-chan
  0

• Can't access common resources public for CUPPA pre-trained classifier

  #603 opened a month ago by weewus
  2

• Invalid reference data error

  #604 opened a month ago by rmapbut
  1

• How to find the known_fusion_db_file files

  #606 opened a month ago by DanielNaro
  1

• cobalt targeted mode null pointer exception

  #512 opened 8 months ago by briankegerreis
  3

• adding SAMvalidation option to LiLAC and TEAL

  #590 opened 2 months ago by nan5895
  3

• LINX Low Copy Number Accuracy

  #601 opened a month ago by amarinderthind
  2

• hmf pipeline for ecdna analysis

  #600 opened a month ago by zhaowsong
  3

• Advice needed in regards to the `gridss_blacklist` within `hmf_dna_pipeline_resources.38_v5.34.tar.gz`

  #573 opened 3 months ago by Teezi
  3

• Representing unmatched PURPLE copy number

  #587 opened 2 months ago by Chunkz616
  5

• java.lang.ClassCastException: class java.util.ArrayList cannot be cast to class java.lang.String

  #570 opened 2 months ago by lipikakalson
  6

• raw copy numbers

  #555 opened 2 months ago by Pranav-Garg
  6

• CNV and LOH analysis for TSO500

  #563 opened 2 months ago by ningb
  1

• Exception in thread "main" java.lang.IllegalArgumentException: No enum constant com.hartwig.hmftools.common.genome.chromosome.HumanChromosome._GL000217.1

  #566 opened 2 months ago by JiwonShon
  1

• Linx annotations results

  #576 opened 2 months ago by zhaowsong
  1

• Purple PoissonDistribution error occurs at negative copyNumber values for regions with somatic SNVs

  #589 opened 2 months ago by tmfreeman400
  3

• Feature Request: Joint CNV Calling

  #593 opened 2 months ago by seedgeorge
  1

• Difference between IMPACT and PAVE_TI in PURPLE vcf file

  #594 opened 2 months ago by HenriettaHolze
  1

• Somatic CNV calling in case of pre-existing CNVs

  #585 opened 2 months ago by HenriettaHolze
  5

• Different Calculation of PURPLE_AF

  #592 opened 2 months ago by Se-Jung-LEE
  4

• Plotting Raw Copy-Number Results

  #579 opened 3 months ago by seedgeorge
  5

• Unable to run COBALT in tumor only mode

  #581 opened 3 months ago by Chunkz616
  1

• GRIPSS running issue

  #572 opened 3 months ago by Teezi
  1

• Length neoepitopes

  #568 opened 3 months ago by p-levy
  2

• CNV results from purple

  #557 opened 4 months ago by zhaowsong
  6

• Sigs for Structural Variants

  #558 opened 4 months ago by amarinderthind
  1

• Driver Catalog File missing

  #556 opened 4 months ago by zhaowsong
  3

• NullPointerException using teal

  #533 opened 5 months ago by elicj01
  3

• SvPrep Depth Annotator missing VCF when no SVs detected

  #540 opened 5 months ago by scwatts
  2

• Replication Timing in the .linx.svs files

  #550 opened 5 months ago by tillyRigby555
  1

• Isofox and Very Polymorphic Human Genes

  #549 opened 5 months ago by DarioS
  6

• NullPointerException for SageApplication

  #547 opened 5 months ago by Tina04021997
  2

• Issue configuring Lilac

  #544 opened 5 months ago by vaksmaz
  1

• Problem running Lilac

  #545 opened 5 months ago by vaksmaz
  1

• FYI: copynumber package removed from Bioconductor >=3.18

  #538 opened 6 months ago by toddajohnson
  0

• Skip faulty CIGARs instead of crashing

  #535 opened 7 months ago by Pranav-Garg
  5

• i cannot find GermlineHetPon.37.vcf.gz in v5_34 resources

  #532 opened 7 months ago by nan5895
  1

• mappability.hdr not found + stitching resource files

  #530 opened 7 months ago by mich-chan
  1

• TEAL error: Exception in thread "main" java.lang.IllegalArgumentException: Comparison method violates its general contract!

  #531 opened 7 months ago by JeanetteCKittel
  1

• GRIPSS: missing sample names error

  #523 opened 7 months ago by Indianhedgehog
  2

• Linx plotting error

  #514 opened 7 months ago by jaesvi
  3

• Latest version of PURPLE is not working with MultiQC

  #524 opened 7 months ago by insilicool
  1

• Tricking SAGE to work with a modified ref genome

  #516 opened 7 months ago by Pranav-Garg
  3

• SAGE Germline files

  #519 opened 7 months ago by Indianhedgehog
  1

• mutect2 PURPLE Compatiblity

  #521 opened 7 months ago by zhaowsong
  1

• mutect2 for purple

  #520 opened 7 months ago by zhaowsong
  0

• TEAL error: Exception in thread "main" java.lang.IllegalArgumentException: Comparison method violates its general contract!

  #518 opened 8 months ago by Ansepil
  5

• Inquiry Regarding Final SV and CNV Results

  #517 opened 8 months ago by zhaowsong
  2

• Hotspots

  #515 opened 8 months ago by mimifp
  2