sigven/pcgr

Issues

• ValueError: invalid literal for int() with base 10: '1.7e+07'

  #252 opened a month ago by sigven
  0

• Most columns are empty within MAF

  #203 opened 2 months ago by weichisyu
  3

• Error in dplyr:semi_join() when only numeric chromosomes in input

  #250 opened 2 months ago by MareikeJaniak
  3

• conda installation issue with ncurses too many levels of symbolic links

  #213 opened 5 months ago by pdiakumis
  0

• Question re. reproducing the example VCF file

  #198 opened 3 months ago by BarryDigby
  7

• control_dp_min is not properly transfered

  #136 opened 3 months ago by gudeqing
  7

• Docker: move to GitHub Container Registry

  #247 opened 4 months ago by pdiakumis
  0

• Conda: deprecate OSX lockfile

  #248 opened 4 months ago by pdiakumis
  0

• run PCGR as non-root user fails at quarto

  #246 opened 4 months ago by HomoPolyethylen
  4

• Issues installing pcgrr in PCGR v2.0.0

  #244 opened 4 months ago by cornejoem
  11

• Docker: decrease image size

  #234 opened 5 months ago by pdiakumis
  0

• expand Clinical biomarkers

  #202 opened 5 months ago by user-tq
  3

• Data bundle update error

  #241 opened 5 months ago by xgnusr
  2

• Extend sample ID length limits

  #224 opened 5 months ago by MareikeJaniak
  5

• Regarding CNV analysis on germline VCF

  #219 opened a year ago by AidanGCr
  4

• Sif image

  #218 opened a year ago by AidanGCr
  2

• Parallel instances

  #214 opened 2 years ago by gitMakeCoffee
  4

• Unable to find some VEP generated predictions

  #204 opened 2 years ago by dattatraymongad
  4

• pcgr-summarise: AttributeError: 'dict' object has no attribute 'INFO'

  #205 opened 2 years ago by pdiakumis
  3

• post-link script failed for package `bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_1`

  #195 opened 2 years ago by pdiakumis
  3

• HLA contigs in vcf files' headers generate error

  #124 opened 3 years ago by V-Catherine
  5

• Add a new biomaker (Amino Acid)

  #138 opened 3 years ago by 1seokyoo
  4

• PCGR error

  #178 opened 3 years ago by adbeggs
  21

• 'names' attribute [20] must be the same length as the vector [18]

  #187 opened 3 years ago by YingYa
  2

• Update R package structure

  #139 opened 3 years ago by pdiakumis
  1

• cyvcf2 not bundled with latest pcgr vesion

  #177 opened 3 years ago by adbeggs
  3

• Feature: use single conda environment for PCGR

  #183 opened 3 years ago by pdiakumis
  0

• PCGR 0.10.15 error

  #180 opened 3 years ago by tinavisnovska
  10

• ALT allele "-" in civic.vcf.gz

  #179 opened 3 years ago by ddrichel
  3

• PCGR data bundle is not compliant with the software version

  #176 opened 3 years ago by adbeggs
  3

• Error: Column `intogen_drivers` not found in `.data`

  #169 opened 3 years ago by YingYa
  1

• error indexing : [E::hts_idx_push] Chromosome blocks not continuous tbx_index_build failed: /workdir/output/91848.pcgr_ready.vcf.gz

  #157 opened 3 years ago by vaishmanobala
  6

• How can I extract EXON and INRON information from vcf INFO tag annotated by the vep with the --numbers parameter?

  #134 opened 3 years ago by QifengSun
  3

• It can't be extracted EXON and INRON information from vcf INFO tag annotated by the vep with --preserved_info_tags EXON,INTRON parameters?

  #135 opened 3 years ago by QifengSun
  1

• share idea of fusion "biomarker_mapping"

  #133 opened 3 years ago by 1seokyoo
  2

• PCGR error

  #132 opened 3 years ago by mano2991
  5

• I geetinng this particular issue while running in grch 37

  #137 opened 3 years ago by mano2991
  6

• TMB from panels

  #131 opened 3 years ago by kokyriakidis
  1

• What does mapping_rank mean in grch37/civic/civic.biomarkers.tsv ？

  #130 opened 3 years ago by sunsong95
  3

• Kataegis, loading data

  #122 opened 3 years ago by brucemoran
  2

• R character strings are limited to 2^31-1 bytes

  #118 opened 3 years ago by YingYa
  7

• tumor ploidy and tumor purity not showing in the report when provided as parameters

  #129 opened 3 years ago by tinavisnovska
  1

• Eitems counting bug - var_eitems by type

  #126 opened 3 years ago by 1seokyoo
  2

• Could pcgr run with singularity

  #128 opened 4 years ago by YingYa
  1

• Failed to install pcgr in R

  #127 opened 4 years ago by Wangxin555
  1

• Unable to get docker image

  #125 opened 4 years ago by ashishyeri
  5

• Data bundle unavailable to download

  #123 opened 4 years ago by ridwan-shaikh
  3

• AD/AF not displaying for tumor only mode

  #119 opened 4 years ago by Shruti-Desai
  5

• "PCGR data bundle is not compliant with the software version"

  #121 opened 4 years ago by V-Catherine
  5

• Download of data bundle

  #120 opened 4 years ago by V-Catherine
  1