berntpopp variant-linker issues

berntpopp / variant-linker

MIT License

0 stars 0 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Enhancement: Add Configuration Validation

#38 berntpopp closed 6 days ago
0
Enhancement: Add Interactive CLI Prompts

#37 berntpopp opened 1 week ago
0
Enhancement: Mapping Output to Schema.org in JSON Format

#36 berntpopp opened 1 week ago
0
Feature Request: Copy Number Variant Support

#35 berntpopp opened 1 week ago
0
Feature request: Enable Streaming Input and Output

#34 berntpopp opened 1 week ago
0
Feature request: Annotate Based on Region or Gene Match

#33 berntpopp opened 1 week ago
0
Feature request: Externalize Hardcoded API Links and Endpoints into Tool Configs

#32 berntpopp opened 1 week ago
0
Feature request: Save Debugging Info to a Log File

#31 berntpopp closed 6 days ago
0
Fix: Fix Debugging Option Not Working with Config File

#30 berntpopp closed 6 days ago
0
Feature request: Add TSV/CSV Output

#29 berntpopp opened 1 week ago
0
Feature request: Cache API Request Responses

#28 berntpopp opened 1 week ago
0
Feature request: Logging of Steps performed

#27 berntpopp closed 6 days ago
0
Feature request: Specify Filtering vs Subsetting

#26 berntpopp opened 1 week ago
0
Bug: Variant Linking Process Fails with Certain VCF Notations

#25 berntpopp closed 2 weeks ago
0
Feature request: Add Debug Messages for Other Scripts

#24 berntpopp closed 2 weeks ago
0
Feature request: Set `merged=1` as a Default Parameter for `vep_params`

#23 berntpopp closed 2 weeks ago
0
Feature request: Set `hgvs=1` as an Additional Default Parameter for `vep_params`

#22 berntpopp closed 2 weeks ago
0
Feature request: Add Support for Configuration File as Parameter Input

#21 berntpopp closed 1 week ago
0
Feature request: Add Semantic Versioning

#20 berntpopp closed 1 week ago
0
Feature request: Migrate Requests to POST Endpoints for Multiple Variants

#19 berntpopp opened 2 weeks ago
0
Feature request: Add Mane and RefSeq Transcript Output

#18 berntpopp closed 2 weeks ago
0
Feature request: Log Requests Sent in Debugging Mode

#17 berntpopp closed 2 weeks ago
0
Feature request: Graceful Error Messages in JSON Format

#16 berntpopp opened 2 weeks ago
0
Feature request: Handle "chr" Prefix in VCF Notation

#15 berntpopp closed 2 weeks ago
0
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 berntpopp closed 2 weeks ago
0
Enhancement: Implement additional parameters for the Variant Recoder in `variantRecoder.js`, with `vcf_string=1` as the default parameter.

#13 berntpopp closed 2 weeks ago
0
Enhancement: Implement a `filterFunction` in `variantLinkerProcessor.js` to allow for flexible filtering of the results before formatting and outputting them.

#12 berntpopp opened 2 weeks ago
1
Testing: Ensure consistency between the output of the Variant-Linker tool and the VEP online version by testing various variants.

#11 berntpopp opened 2 weeks ago
2
Feature request: Determine if there is a specific setting for annotating variant frequencies (gnomAD/gnomADg data) in the VEP API.

#10 berntpopp closed 2 weeks ago
1
Enhancement: Add the ability to specify the genome build reference (hg19/hg38) for annotations in the Variant-Linker tool.

#9 berntpopp opened 2 weeks ago
1
Bug: Running the tool with the variant `ENST00000302118:c.137G>A` results in an error: "Error: Cannot read properties of undefined (reading 'hgvsc')".

#8 berntpopp closed 2 weeks ago
2
Bug: The genomic annotation in VCF format is not functioning correctly for certain variants, e.g., `1-55051215-G-GA`.

#7 berntpopp closed 2 weeks ago
3
Enhancement: Improve the handling of non-coding variants in the Variant-Linker tool.

#6 berntpopp closed 2 weeks ago
2
Enhancement: Add comprehensive test cases to ensure the robustness of the Variant-Linker tool.

#5 berntpopp opened 2 weeks ago
0
Feature request: Implement Optional parameters for VEP annotation

#4 berntpopp closed 2 weeks ago
0
Feature request: Integrate local versions of VEP (Variant Effect Predictor) and Variant Recoder into `variant-linker`

#3 berntpopp opened 3 months ago
0
Feature request: Extend `variant-linker` to support input and output in VCF (Variant Call Format) files.

#2 berntpopp opened 3 months ago
0
Feature Request: Implement scoring functionality in `variant-linker` to calculate meta scores based on the VEP annotations obtained.

#1 berntpopp closed 1 week ago
3