#447 - implement babelfish for VCF #660
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reece
reviewed
Jun 14, 2023
… that shadows builtin
…apper from class. People can do that themselves and control whether they want validation etc
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Hi @reece are you able to review? Afterwards I'll start on the parser and do as a separate PR |
…lt. Add to test case ability to test alternative VCFs that go to same g. HGVS
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#447 - Implement hgvs babelfish for VCF
Also fixes
#616 - Babelfish hardcoded GRCh38
I changed the test expected VCF results - my reasoning follows:
NC_000006.12:g.49949407=
Old: None
New: ("6", 49949407, "A", ".", 'identity')
Notes: As we can now load VCFs, this is now symmetrical (ie can convert to and back again w/o change). You can represent an identity/no change this way in VCF or by repeating the ref, I went with '.' but feel free to change
The other changes involve VT parsimony rules - https://genome.sph.umich.edu/wiki/Variant_Normalization
"A variant has superfluous nucleotides on its left side if the leftmost nucleotide of each variant is of the same type and the removal of the nucleotide from each allele will not result in an empty allele."
NC_000006.12:g.49949407A>T
Old: ("6", 49949406, "AA", "AT", "sub")
New: ("6", 49949407, "A", "T", "sub")
NC_000006.12:g.49949413_49949414delinsCC
Old: ("6", 49949412, "AAA", "ACC", "delins")
New: ("6", 49949413, "AA", "CC", "delins")