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View Code? Open in Web Editor NEWvcf2hl7v2: a utility to convert VCF files into HL7 V2 format for genomics-EHR integration
License: Apache License 2.0
vcf2hl7v2: a utility to convert VCF files into HL7 V2 format for genomics-EHR integration
License: Apache License 2.0
Please answer the following questions for yourself before submitting an issue.
The file(geneKB_Gene_table.csv
) is too large to be submitted with the binary. Think of a way to optimize the usage of this file or an alternate way to populate the Gene Studied OBX.
The current code uses the gene geneKB_Gene_table.csv
to populate the Gene Studied OBX.
Please answer the following questions for yourself before submitting an issue.
The current installation guide points to the test PyPI URL. We need to update the installation guide when we release vcf2hl7v2 on PyPI.
Update the installation guide when we release vcf2hl7v2 on PyPI.
Installation guide points to the test PyPI URL.
Please answer the following questions for yourself before submitting an issue.
sourceClass defaults to 'germline' and is a required field
remove sourceClass default, and make it an optional field.
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latest
macOS
Set up dependabot
for automatic dependency updates.
Dependency update is not considered.
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Add support for the conversion of Structural Variants.
The current code supports the conversion of simple variants (SNVs, Indels), along with zygosity and phase relationships, for autosomes, sex chromosomes, and mitochondrial DNA.
Please answer the following questions for yourself before submitting an issue.
Add documentation for vcf2hl7v2.
Consider both, ALT allele depth and REF allele depth and use the major allele for Homoplasmic vs Heteroplasmic.
We consider only ALT allele depth for Homoplasmic vs Heteroplasmic
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