kishwarshafin/pepper

Issues

• PEPPER-Margin-DeepVariant takes more cores than limit

  #208 opened 5 months ago by martabaragli
  1

• Error in margin phase :No valid VCF entries found!

  #207 opened 6 months ago by kch4221
  0

• generated haplotagged BAM file

  #206 opened 7 months ago by nikhita-damaraju
  0

• Issue with docker GPU

  #205 opened 8 months ago by martabaragli
  0

• phasing between R9 and R10 data

  #204 opened 9 months ago by Yijun-Tian
  0

• Can pepper be used for short contigs?

  #203 opened 10 months ago by zhan4429
  0

• Samples w/older guppy

  #202 opened 10 months ago by dmjask
  0

• Model for Guppy 6.5.7 SUP and/or Dorado 0.34

  #193 opened a year ago by gchevignon
  1

• Do I have to train a model for specific organism ?

  #200 opened 10 months ago by Modernism-01
  0

• resuming the run

  #189 opened a year ago by Shruti-BioCode
  1

• Snp prediction accuracy is low in all difficult mapping areas

  #199 opened a year ago by oranges7
  1

• Joint Genotyping Recommendation

  #198 opened a year ago by SophieS9
  0

• ImportError with Singularity

  #196 opened a year ago by aCoalBall
  0

• Root privileges

  #195 opened a year ago by Meer9234
  0

• MARGIN using param file for older model

  #194 opened a year ago by thainsCEB
  0

• Dockerfile

  #192 opened a year ago by yneuma
  0

• Installation issue with pytorch

  #184 opened 2 years ago by noncodo
  1

• HiFi_variant_calling tutorial inconsistent

  #190 opened a year ago by splaisan
  0

• Could not read from reference fasta file.

  #188 opened 2 years ago by sinha-shruti
  1

• Issues while trying use the singularity image

  #187 opened 2 years ago by kiratalreja3
  0

• Deepvariant pepper settings for duplex calling

  #186 opened 2 years ago by alvinwt
  0

• KeyError: "Unable to open object (object 'predictions' doesn't exist)"

  #185 opened 2 years ago by hannahgoldswain
  0

• am I running this wrong?

  #183 opened 2 years ago by shinlin77
  7

• Local PEPPER installation for variant calling

  #179 opened 2 years ago by leonorpalmeira
  4

• Can you make pepper available on conda, please?

  #182 opened 2 years ago by yuukiiwa
  1

• Disabling dawnsampling in pepper_margin_deepvariant ?

  #178 opened 2 years ago by kiflu-23
  4

• Ambiguous IUPAC bases appearing in output VCF violate VCF Spec

  #167 opened 2 years ago by rickymagner
  4

• Phasing into a single phaseset across targeted region of interest

  #172 opened 2 years ago by smf96
  6

• Calloc issue with docker even after allocating memory - margin polish

  #180 opened 2 years ago by sofiabanu
  1

• pysam not working

  #170 opened 2 years ago by Az513
  1

• Seq2Seq_atn.py

  #176 opened 2 years ago by ElaheA90
  1

• DeepVariant Step Error: PythonNext() argument variant is not valid: Dynamic cast failed

  #174 opened 2 years ago by weilu1998
  3

• ./. GQ=0 in gvcf where I have high coverage as homozygous reference

  #175 opened 2 years ago by aguygarner
  1

• issue in running Pepper

  #173 opened 2 years ago by tahashmi
  1

• .csi indexing when phasing

  #169 opened 2 years ago by aguygarner
  4

• ERROR: basic_string::substr

  #168 opened 2 years ago by chilampoon
  4

• optimal GPU type

  #164 opened 2 years ago by COMInterop
  1

• not producing PEPPER_HP_OUTPUT_2.vcf.gz output for sample data pepper polishing (v.04)

  #177 opened 2 years ago by plnspineda
  0

• g.vcf

  #181 opened 2 years ago by shinlin77
  1

• Margin-[E::hts_open_format] Failed to open file .bam

  #161 opened 2 years ago by infotmatician
  3

• Depth differences between r0.5 and r0.8

  #166 opened 2 years ago by VLeducq
  3

• Critical Vulnerabilities in the published Docker image

  #171 opened 2 years ago by rberg2
  2

• Genotype quality graph always 0

  #165 opened 2 years ago by cdebuck
  1

• Setting Guppy version

  #163 opened 2 years ago by vladimirsouza
  5

• ImportError

  #159 opened 2 years ago by BrendaLee1
  1

• RefCall vs. PASS

  #160 opened 2 years ago by yifeng-evo
  3

• run error on run_deepvariant.py

  #162 opened 2 years ago by windforclouds
  0

• Model training data

  #158 opened 2 years ago by mproberts99
  2

• No valid VCF entries found!

  #157 opened 2 years ago by infotmatician
  4

• AD field looks wierd

  #156 opened 2 years ago by Yijun-Tian
  5