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Use a known normalization algorithm in utils.hgvs._normalized_vcf function #140

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erikyao opened this issue Jan 5, 2022 · 0 comments
Open

Use a known normalization algorithm in utils.hgvs._normalized_vcf function #140

erikyao opened this issue Jan 5, 2022 · 0 comments
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@newgene @erikyao

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erikyao commented Jan 5, 2022 •
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There are a few VCF normalization tools/algorithms that can be used in our _normalized_vcf function, e.g.:

Our current implementation fails to meet the Parsimony definition of VCF normalization:

A variant is parsimonious if and only if it is represented in as few nucleotides as possible
without an allele of length 0.

E.g. our current implementation cannot handle cases like ref = "TCCCCT", alt = "CCCCT". Normalized sequences should be ref = 'TC', alt = 'C'.
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