hgvs
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Consider exposing a utility for converting between g. variants by leveraging pyliftover
Workaround using the existing functionality: If I have, say var_g
= hgvs.parser.Parser().parse_hgvs_variant('NC_000005.9:g.112090651A>G')
and I want to do liftover between assemblies, one way that seems to work is to call vm.relevant_transcripts(var_g)
and pick a random relevant transcript (that starts with NM_
) using the GRCh38
AssemblyMapper
, then do var_c = vm.g_to_c(parsed_variant, relevant_transcript)
and then use the AssemblyMapper
associated with GRCh37
to call c_to_g(var_c)
. However, it feels clunky and I'm not sure if picking a random "relevant transcript" makes sense in the general case.
Thank you @rhdolin for figuring out this workaround!