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scholl-lab
/
vcf-filtering
A collection of scripts for filtering annotated variant call format files
MIT License
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Bug: Empty Outputs in Tumor-Only Analysis with Numbered GEN[1] Fields
#54
berntpopp
opened
3 days ago
0
Bug: Fields with Commas Converted to Numbers in Excel
#53
berntpopp
opened
3 days ago
0
Bug: Improve Debug Level Implementation for Clarity and Consistency
#52
berntpopp
opened
3 days ago
0
Feature Request: Allow Filtering for All Genes
#51
berntpopp
closed
3 days ago
0
Bug: Fixed output separator causing Excel conversion issues
#50
berntpopp
opened
4 days ago
0
Bug: Samples file required even if empty, causing pipeline failure
#49
berntpopp
opened
4 days ago
0
Bug: Incorrect output file format when specifying XLSX output without output file
#48
berntpopp
opened
4 days ago
0
Bug: Genotypes Not Added in replace_gt_with_sample.sh When Using Probands File
#47
berntpopp
opened
1 week ago
0
Feature request: Handle Non-1 GT Fields in replace_gt_with_sample.sh
#46
berntpopp
closed
1 week ago
0
Feature request: Add Error Tolerance and Debugging Level to Main Script
#45
berntpopp
closed
3 days ago
0
Feature request: Keep BED Files in a Temporary Folder for Reuse
#44
berntpopp
closed
1 week ago
0
Feature request: Change workflow to allow a unified sample file
#43
berntpopp
opened
1 week ago
0
Tests: Add tests to all scripts and add test data
#42
berntpopp
opened
1 week ago
0
Feature request: Add option to expand gene interval
#41
berntpopp
closed
1 week ago
0
Tests: Check all flags for functionality
#40
berntpopp
opened
1 week ago
0
Bug: Edge case 0/2 in GT field and G,A in Alt fields
#39
berntpopp
closed
1 week ago
0
Feature request: Add Option for Probands and Controls in replace_gt_with_sample
#38
berntpopp
closed
1 week ago
1
Feature request: Filtering Presets for Main Script
#37
berntpopp
opened
1 week ago
0
Feature request: Investigate multiple VCFs as input
#36
berntpopp
opened
3 weeks ago
1
Feature request: Conda env as parameter
#35
berntpopp
opened
3 weeks ago
0
Feature request: Use Phenopackets for HPO filtering input
#34
berntpopp
opened
3 weeks ago
0
Documentation: Add Installation Instructions for All Required Tools
#33
berntpopp
opened
1 month ago
0
Feature Request: Add Script to Generate IGV Browser Screenshots
#32
berntpopp
opened
1 month ago
1
Documentation: Add Detailed Examples for All Scripts
#31
berntpopp
opened
1 month ago
0
Documentation: Update README and Usage Description with Examples for All Scripts
#30
berntpopp
opened
1 month ago
0
Enhancement: Add Option to Filter by Position or Specific Variants
#29
berntpopp
opened
1 month ago
1
Enhancement: Add Interactive CLI Prompts
#28
berntpopp
opened
1 month ago
0
Documentaion: Filter Logic and Available Annotations
#27
berntpopp
opened
1 month ago
0
Refactor: main script in main folder and helpers in subfolders
#26
berntpopp
opened
1 month ago
0
Documentation: add installation instruction
#25
berntpopp
opened
1 month ago
0
Feature request: add option to perform gene burden analysis
#24
berntpopp
opened
1 month ago
3
Feature request: add counts for individuals with a specific variant
#23
berntpopp
closed
1 week ago
1
Feature request: add check if the Gene name was found
#22
berntpopp
closed
1 week ago
0
Feature request: Add links to documentation, repository and help email
#21
berntpopp
closed
1 week ago
0
Feature request: Add version information of other tools to logging
#20
berntpopp
closed
1 week ago
0
Feature request: Configurable delimiters in filter_variants.sh
#19
berntpopp
opened
8 months ago
0
long options handling not implemented for all in filter_phenotypes.sh
#18
berntpopp
closed
8 months ago
0
Bug: Check Input files format in replace GT script
#17
berntpopp
closed
1 week ago
0
Feature request: Statistics for the filtered table
#16
berntpopp
opened
8 months ago
1
Add a script to generate screenshots for visual validation
#15
berntpopp
opened
8 months ago
1
Add option to filter by position or for specific variants instead of gene name
#14
berntpopp
opened
8 months ago
1
Add installation instructions for all required tools
#13
berntpopp
opened
8 months ago
1
Update README and usage description with examples for all scripts
#12
berntpopp
opened
8 months ago
1
Make tsv_to_excel.R more generic
#11
berntpopp
closed
8 months ago
0
Implement sheet handling in tsv_to_excel.R script
#10
berntpopp
closed
8 months ago
0
tsv_to_excel.R location is currently hardcoded in filter_variants.sh
#9
berntpopp
closed
8 months ago
0
add script name to version echo in all script
#8
berntpopp
closed
8 months ago
0
The replace_gt_with_sample.sh script currently has no semantic versioning
#7
berntpopp
closed
8 months ago
0
Implement filter_phenotypes.sh in filter_variants.sh
#6
berntpopp
opened
8 months ago
0
Add an argument to set the separator in the replace_gt_with_sample.sh script and change default
#5
berntpopp
closed
8 months ago
0
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