HKU-BAL/Clair

Issues

• error using on HPC

  #66 opened 3 years ago by myonaung
  1

• Running issue!!

  #69 opened 2 years ago by g-s-2018
  0

• GVCF output

  #38 opened 4 years ago by GuillaumeHolley
  6

• cram file support ?

  #67 opened 3 years ago by YanfengJi
  1

• downsampled BAM cannot download

  #64 opened 3 years ago by shiying-sxu
  1

• Clair force calling using callVarBam calls more number of variants than included in a vcf file.

  #65 opened 3 years ago by teketelah
  3

• Models for guppy v5 basecalled Nanopore data

  #60 opened 3 years ago by flashton2003
  1

• Quality cut off determination for CLR data

  #56 opened 3 years ago by agos316
  1

• train clair with single strands?

  #22 opened 3 years ago by marcotoffoli
  3

• sars-cov2 model

  #59 opened 3 years ago by shimbalama
  1

• HETEROSNP is not defined in the header

  #62 opened 3 years ago by champ1994
  1

• Which Reference to use during Training?

  #63 opened 3 years ago by champ1994
  1

• ONT R9.4.1 vs R10.3

  #61 opened 3 years ago by fidibidi
  1

• Any chance of a clair model trained on guppy >=3.6.0, and on guppy 4.4.2 with bonito?

  #54 opened 3 years ago by oneillkza
  4

• problem during training

  #57 opened 3 years ago by huangnengCSU
  1

• ValueError: invalid literal for int() with base 10: 'CCA'

  #55 opened 4 years ago by KewinOgink
  1

• Demo Error: Missing testingData

  #53 opened 4 years ago by Eurus-Holmes
  2

• quality threshold advice

  #49 opened 4 years ago by RichardCorbett
  1

• Automatically call SNPs for all contigs in fasta file?

  #51 opened 4 years ago by OscarAspelin
  2

• model quantization experiments

  #52 opened 4 years ago by ramcn
  2

• Clair and Clairvoyante having trouble with bam file from human transcript alignments

  #50 opened 4 years ago by rainwala
  1

• Specific use case

  #48 opened 4 years ago
  1

• SNV force calling

  #45 opened 4 years ago by vollrath-p
  2

• filtering an ONT VCF Clair generated callset from a bi-modal result

  #46 opened 4 years ago by sbilobram
  1

• Source of input BAM file?

  #47 opened 4 years ago by ChristopherRichie
  1

• Bioconda Installation Issues - Error: samtoolssamtools: error while loading shared libraries: libcrypto.so.1.0.0

  #44 opened 4 years ago by zhemingfan
  1

• Memory problem

  #42 opened 4 years ago by Francesc-Muyas
  1

• PacBio Subread Data

  #41 opened 4 years ago by agos316
  2

• clair and ONT samples aligned with hg19

  #43 opened 4 years ago by sbilobram
  5

• clarification on -dcov option

  #40 opened 4 years ago by marcotoffoli
  1

• trained clair model taking long time to run

  #39 opened 4 years ago by kevyin
  1

• Installing without conda nor docker

  #36 opened 4 years ago by arturo-opsetmoen-amador
  1

• KeyError: '*T'

  #35 opened 4 years ago by loof91
  5

• Number of needed tensors to be processed

  #34 opened 4 years ago by sinamajidian
  2

• An error when run it.

  #32 opened 4 years ago by ERICBJ2020
  1

• Error when take the output vcf as input for VariantQC

  #33 opened 4 years ago by snower2010
  2

• Trouble when reproduce the

  #29 opened 4 years ago by snower2010
  2

• clair can not find model.meta

  #31 opened 4 years ago by harazono
  1

• Guppy base called using flipflop model

  #30 opened 4 years ago by vahidAK
  1

• wget '500 Internal Server Error' when downloading training models

  #28 opened 5 years ago by frabanal
  2

• --haploid setting less sensitive than default

  #24 opened 5 years ago by NatPRoach
  3

• VCF reporting for haploid samples

  #17 opened 5 years ago by OscarAspelin
  2

• Coverage is less than igv show

  #25 opened 5 years ago by zhenLiuXplr
  3

• Interpretation of quality scores

  #27 opened 5 years ago by flashton2003
  1

• How to handle such "duplicate" calls?

  #15 opened 5 years ago by SHuang-Broad
  3

• Can I use the model training on PacBio CCS data for PacBio non-CCS data?

  #26 opened 5 years ago by flashton2003
  2

• Output monomorphic sites when used with Known variant vcf

  #23 opened 5 years ago by jd3234
  2

• Somatic and germline

  #19 opened 5 years ago by vahidAK
  2

• SNP/indel tag in vcf

  #18 opened 5 years ago by pristanna
  2

• Alarm

  #14 opened 5 years ago by shimbalama
  1