varity.hgvs-to-vcf — varity 0.4.1

Functions to convert HGVS into VCF-style variants.

hgvs->vcf-variants clj multimethod

(hgvs->vcf-variants hgvs ref-seq ref-gene)

(hgvs->vcf-variants hgvs gene ref-seq ref-gene)

Converts cDNA/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-cdna-hgvs clj multimethod

(protein-hgvs->vcf-variants-with-cdna-hgvs hgvs ref-seq ref-gene)

(protein-hgvs->vcf-variants-with-cdna-hgvs hgvs gene ref-seq ref-gene)

Converts protein HGVS into possible VCF-style variants and cDNA 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 :cdna}.