scholl-lab/vcf-filtering

Issues

• Feature request: Investigate multiple VCFs as input

  #36 opened 2 days ago
  1

• Feature request: Conda env as parameter

  #35 opened 2 days ago
  0

• Feature request: Use Phenopackets for HPO filtering input

  #34 opened 2 days ago
  0

• Documentation: Add Installation Instructions for All Required Tools

  #33 opened 7 days ago
  0

• Feature Request: Add Script to Generate IGV Browser Screenshots

  #32 opened 7 days ago
  0

• Documentation: Add Detailed Examples for All Scripts

  #31 opened 7 days ago
  0

• Documentation: Update README and Usage Description with Examples for All Scripts

  #30 opened 7 days ago
  0

• Enhancement: Add Option to Filter by Position or Specific Variants

  #29 opened 7 days ago
  0

• Enhancement: Add Interactive CLI Prompts

  #28 opened 7 days ago
  0

• Documentaion: Filter Logic and Available Annotations

  #27 opened 7 days ago
  0

• Refactor: main script in main folder and helpers in subfolders

  #26 opened 10 days ago
  0

• Documentation: add installation instruction

  #25 opened 10 days ago
  0

• Feature request: add option to perform gene burden analysis

  #24 opened 10 days ago
  2

• Feature request: add counts for individuals with a specific variant

  #23 opened 10 days ago
  1

• Feature request: add check if the Gene name was found

  #22 opened 10 days ago
  0

• Add links to documentation, repository and help email

  #21 opened 7 months ago
  0

• Add version information of other tools to logging

  #20 opened 7 months ago
  0

• Configurable delimiters in filter_variants.sh

  #19 opened 7 months ago
  0

• long options handling not implemented for all in filter_phenotypes.sh

  #18 opened 7 months ago
  0

• Check Input files format in replace GT script

  #17 opened 7 months ago
  0

• Statistics for the filtered table

  #16 opened 7 months ago
  0

• Add a script to generate screenshots for visual validation

  #15 opened 7 months ago
  1

• Add option to filter by position or for specific variants instead of gene name

  #14 opened 7 months ago
  1

• Add installation instructions for all required tools

  #13 opened 7 months ago
  1

• Update README and usage description with examples for all scripts

  #12 opened 7 months ago
  1

• Make tsv_to_excel.R more generic

  #11 opened 7 months ago
  0

• Implement sheet handling in tsv_to_excel.R script

  #10 opened 7 months ago
  0

• tsv_to_excel.R location is currently hardcoded in filter_variants.sh

  #9 opened 7 months ago
  0

• add script name to version echo in all script

  #8 opened 7 months ago
  0

• The replace_gt_with_sample.sh script currently has no semantic versioning

  #7 opened 7 months ago
  0

• Implement filter_phenotypes.sh in filter_variants.sh

  #6 opened 7 months ago
  0

• Add an argument to set the separator in the replace_gt_with_sample.sh script and change default

  #5 opened 7 months ago
  0

• Add a sheet with Meta information to the XLSX output

  #4 opened 7 months ago
  2

• The replace_gt_with_sample.sh script currently has no help message

  #3 opened 7 months ago
  0

• Add an argument to pass arguments to the replace_script in the filter_variants.sh script

  #2 opened 7 months ago
  0

• config setting should have priority over defaults set in the filter_variants.sh script

  #1 opened 7 months ago
  0