berntpopp/variant-linker

Issues

• Feature request: Make variant-linker a package that can be added into other projetcs

  #41 opened 2 months ago by berntpopp
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• Bug: response differs when giving a transcript or genomic input

  #40 opened 2 months ago by berntpopp
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• Bug: meta score calculation not working consistently

  #39 opened 2 months ago by berntpopp
  1

• Enhancement: Mapping Output to Schema.org in JSON Format

  #36 opened 6 months ago by berntpopp
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• Feature Request: Copy Number Variant Support

  #35 opened 6 months ago by berntpopp
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• Feature request: Enable Streaming Input and Output

  #34 opened 6 months ago by berntpopp
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• Feature request: Add TSV/CSV Output

  #29 opened 6 months ago by berntpopp
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• Feature request: Cache API Request Responses

  #28 opened 6 months ago by berntpopp
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• Feature request: Externalize Hardcoded API Links and Endpoints into Tool Configs

  #32 opened 6 months ago by berntpopp
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• Feature request: Annotate Based on Region or Gene Match

  #33 opened 6 months ago by berntpopp
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• Feature request: Migrate Requests to POST Endpoints for Multiple Variants

  #19 opened 6 months ago by berntpopp
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• Feature request: Specify Filtering vs Subsetting

  #26 opened 6 months ago by berntpopp
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• Enhancement: Implement a `filterFunction` in `variantLinkerProcessor.js` to allow for flexible filtering of the results before formatting and outputting them.

  #12 opened 6 months ago by berntpopp
  1

• Enhancement: Add Configuration Validation

  #38 opened 6 months ago by berntpopp
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• Fix: Fix Debugging Option Not Working with Config File

  #30 opened 6 months ago by berntpopp
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• Feature request: Logging of Steps performed

  #27 opened 6 months ago by berntpopp
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• Feature request: Save Debugging Info to a Log File

  #31 opened 6 months ago by berntpopp
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• Enhancement: Add Interactive CLI Prompts

  #37 opened 6 months ago by berntpopp
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• Testing: Ensure consistency between the output of the Variant-Linker tool and the VEP online version by testing various variants.

  #11 opened 6 months ago by berntpopp
  2

• Feature request: Add Support for Configuration File as Parameter Input

  #21 opened 6 months ago by berntpopp
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• Feature request: Add Semantic Versioning

  #20 opened 6 months ago by berntpopp
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• Feature Request: Implement scoring functionality in `variant-linker` to calculate meta scores based on the VEP annotations obtained.

  #1 opened 6 months ago by berntpopp
  3

• Bug: Variant Linking Process Fails with Certain VCF Notations

  #25 opened 6 months ago by berntpopp
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• Feature request: Add Debug Messages for Other Scripts

  #24 opened 6 months ago by berntpopp
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• Feature request: Log Requests Sent in Debugging Mode

  #17 opened 6 months ago by berntpopp
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• Feature request: Handle "chr" Prefix in VCF Notation

  #15 opened 6 months ago by berntpopp
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• Feature request: Add Mane and RefSeq Transcript Output

  #18 opened 6 months ago by berntpopp
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• Feature request: Set `hgvs=1` as an Additional Default Parameter for `vep_params`

  #22 opened 6 months ago by berntpopp
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• Feature request: Set `merged=1` as a Default Parameter for `vep_params`

  #23 opened 6 months ago by berntpopp
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• Enhancement: Add the ability to specify the genome build reference (hg19/hg38) for annotations in the Variant-Linker tool.

  #9 opened 6 months ago by berntpopp
  1

• Feature request: Determine if there is a specific setting for annotating variant frequencies (gnomAD/gnomADg data) in the VEP API.

  #10 opened 6 months ago by berntpopp
  1

• Feature request: Graceful Error Messages in JSON Format

  #16 opened 6 months ago by berntpopp
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• Enhancement: Improve the handling of non-coding variants in the Variant-Linker tool.

  #6 opened 6 months ago by berntpopp
  2

• Bug: Running the tool with the variant `ENST00000302118:c.137G>A` results in an error: "Error: Cannot read properties of undefined (reading 'hgvsc')".

  #8 opened 6 months ago by berntpopp
  2

• Bug: The genomic annotation in VCF format is not functioning correctly for certain variants, e.g., `1-55051215-G-GA`.

  #7 opened 6 months ago by berntpopp
  3

• Enhancement: Improve the stability of the annotation process by using genomic coordinates instead of HGVS. This will involve several steps, including using the region endpoint, converting VCF notation, and adding VCF detection.

  #14 opened 6 months ago by berntpopp
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• Enhancement: Implement additional parameters for the Variant Recoder in `variantRecoder.js`, with `vcf_string=1` as the default parameter.

  #13 opened 6 months ago by berntpopp
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• Feature request: Implement Optional parameters for VEP annotation

  #4 opened 6 months ago by berntpopp
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• Enhancement: Add comprehensive test cases to ensure the robustness of the Variant-Linker tool.

  #5 opened 6 months ago by berntpopp
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• Feature request: Integrate local versions of VEP (Variant Effect Predictor) and Variant Recoder into `variant-linker`

  #3 opened 9 months ago by berntpopp
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• Feature request: Extend `variant-linker` to support input and output in VCF (Variant Call Format) files.

  #2 opened 9 months ago by berntpopp
  0