HKU-BAL/ClairS

Issues

• Only 1 somatic variant returned

  #34 opened 3 months ago by Jiayi-Wang-Joey
  2

• Very few somatic variants in output VCF

  #36 opened 3 months ago by mdehankar3
  1

• NumPY error when installed thru singularity and conda

  #35 opened 3 months ago by ccbruels
  1

• Question: Timeline for releasing new models

  #33 opened 4 months ago by lucy924
  4

• Loci file /opt/conda/envs/clairs/bin/cnv_data/reference_files/loci_files/G1000_loci_hg38_chr1.txt does not appear to exist.

  #32 opened 5 months ago by erdikilic
  4

• samtools index: failed to open error

  #28 opened 5 months ago by DIPLOMICS-SA
  9

• Adding Normal Sample GT to the VCF file

  #27 opened 5 months ago by bcantarel
  3

• ClairS quits with exit code 0 but no output, no error logged

  #25 opened 5 months ago by nparmalee
  5

• ClairS crashing with spaces in input file name

  #23 opened 5 months ago by RenzoTale88
  2

• Enhancing somatic variant calling and execution speed

  #22 opened 5 months ago by sloth-eat-pudding
  5

• Questions Regarding Heterozygous Variants, Somatic Mutations, and Phasing in ClairS Usage

  #18 opened 5 months ago by sloth-eat-pudding
  4

• tmp folders not being deleted after calling

  #24 opened 8 months ago by A-Goretsky
  2

• add v4.3.0 model for clair3 params

  #19 opened 9 months ago by bakeronit
  6

• sh files for data preprocessing

  #20 opened 9 months ago by shiying-sxu
  1

• Question in training data label generation code - get_candidates.py

  #21 opened 10 months ago by quito418
  2

• [Inquiry for train dataset generation procedure]

  #17 opened a year ago by quito418
  2

• [Ask for insights on Illumina results regarding ClairS workflow/design choices]

  #15 opened a year ago by quito418
  5

• Docker latest version

  #14 opened a year ago by husamia
  1

• Question: comparison with DRAGEN Somatic

  #13 opened a year ago by husamia
  1

• Bam files for SEQC2 samples

  #4 opened a year ago by KeyTals
  1

• Germline variants present in output.vcf

  #12 opened a year ago by xingyaoc
  1

• Nondeterminism in ClairS output

  #11 opened a year ago by xingyaoc
  1

• question: model for 5khz data

  #10 opened a year ago by bakeronit
  4

• Training for PacBio HiFi indel calling

  #9 opened 2 years ago by proteinosome
  11

• Haplotype filtering step keep stuck

  #8 opened 2 years ago by tahashmi
  4

• Option to call SNPs only

  #6 opened 2 years ago by xingyaoc
  1

• Interpreting the QUAL column

  #1 opened 2 years ago by zhemingfan
  2

• select_hetero_snp_for_phasing breaks for contigs where no variants are found

  #5 opened 2 years ago by xingyaoc
  3

• Running with singularity

  #3 opened 2 years ago by jaesvi
  2

• Empty VCF produced by ClairS

  #2 opened 2 years ago by rowanhowellGE
  2