varity.hgvs-to-vcf
Functions to convert HGVS into VCF-style variants.
hgvs->vcf-variants
multimethod
(hgvs->vcf-variants hgvs ref-seq ref-gene)(hgvs->vcf-variants hgvs gene ref-seq ref-gene)
Converts coding DNA/protein hgvs into possible VCF-style variants. Transcript of
hgvs, such as NM_005228, is used for ref-genes search. Alternatively, gene,
such as EGFR, can be used if transcript does not exist. ref-seq must be a path
to reference or an instance which implements
cljam.io.protocols/ISequenceReader. ref-gene must be a path to
refGene.txt(.gz), ref-gene index, or a ref-gene entity. A returned sequence
consists of {:chr :pos :ref :alt}.protein-hgvs->vcf-variants-with-coding-dna-hgvs
multimethod
(protein-hgvs->vcf-variants-with-coding-dna-hgvs hgvs ref-seq ref-gene)(protein-hgvs->vcf-variants-with-coding-dna-hgvs hgvs gene ref-seq ref-gene)
Converts protein HGVS into possible VCF-style variants and coding DNA HGVS.
Transcript of hgvs, such as NM_005228, is used for ref-genes search.
Alternatively, gene, such as EGFR, can be used if transcript does not exist.
ref-seq must be a path to reference or an instance which implements
cljam.io.protocols/ISequenceReader. ref-gene must be a path to
refGene.txt(.gz), ref-gene index, or a ref-gene entity. A returned sequence
consists of {:vcf :coding-dna}.