Variant linking process over VCF fails with certain notations (e.g., ENST00000650946.1:n.439-1601_439-1600insC)
Description:
The variant linking process fails when using certain VCF notations, resulting in the error message: "No valid VCF string found in Variant Recoder response". This issue is observed when running the tool with the variant ENST00000650946.1:n.439-1601_439-1600insC.
Steps to Reproduce:
Run the tool with the following command:
variant-linker --variant 'ENST00000650946.1:n.439-1601_439-1600insC' -d
Observe the error message:
variant-linker:main Error in main variant analysis process: No valid VCF string found in Variant Recoder response +1ms
Error: No valid VCF string found in Variant Recoder response
Expected Behavior:
The tool should correctly process the variant and return the expected annotations.
Actual Behavior:
The tool fails with the error: "No valid VCF string found in Variant Recoder response".
Proposed Solution:
Investigate the source of the error in the variant linking process, specifically the handling of VCF strings returned by the Variant Recoder.
Ensure that the tool correctly processes VCF strings and does not fail when encountering certain notations.
Add additional checks to handle cases where VCF strings might be formatted differently or contain multiple entries.
Acceptance Criteria:
The tool correctly processes the variant ENST00000650946.1:n.439-1601_439-1600insC.
The error "No valid VCF string found in Variant Recoder response" is resolved.
Tests are added to verify the processing of similar variants.
Variant linking process over VCF fails with certain notations (e.g., ENST00000650946.1:n.439-1601_439-1600insC)
Description: The variant linking process fails when using certain VCF notations, resulting in the error message: "No valid VCF string found in Variant Recoder response". This issue is observed when running the tool with the variant ENST00000650946.1:n.439-1601_439-1600insC.
Steps to Reproduce:
Run the tool with the following command: variant-linker --variant 'ENST00000650946.1:n.439-1601_439-1600insC' -d
Observe the error message: variant-linker:main Error in main variant analysis process: No valid VCF string found in Variant Recoder response +1ms Error: No valid VCF string found in Variant Recoder response
Expected Behavior: The tool should correctly process the variant and return the expected annotations.
Actual Behavior: The tool fails with the error: "No valid VCF string found in Variant Recoder response".
Proposed Solution: Investigate the source of the error in the variant linking process, specifically the handling of VCF strings returned by the Variant Recoder. Ensure that the tool correctly processes VCF strings and does not fail when encountering certain notations. Add additional checks to handle cases where VCF strings might be formatted differently or contain multiple entries. Acceptance Criteria:
The tool correctly processes the variant ENST00000650946.1:n.439-1601_439-1600insC. The error "No valid VCF string found in Variant Recoder response" is resolved. Tests are added to verify the processing of similar variants.