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varity.vcf-to-hgvs

Functions to convert a VCF-style variant into HGVS.

select-variant

(select-variant var seq-rdr rg)
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vcf-variant->coding-dna-hgvs
multimethod
(vcf-variant->coding-dna-hgvs variant ref-seq ref-gene)(vcf-variant->coding-dna-hgvs variant ref-seq ref-gene options)
Converts a VCF-style variant (:chr, :pos, :ref, and :alt) into coding DNA HGVS.
alt must be a single alternation such as "TG". "TG,T", for example, is not
allowed. 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 coding DNA HGVS defined in clj-hgvs.

Options:

  :prefer-deletion?  Prefer deletion (e.g. "c.7_9del") to repeated
                     sequences (e.g. "c.4_6[1]"), default false.

  :prefer-insertion? Prefer insertion (e.g. "c.9_10insAGG") to repeated
                     sequences (e.g. "c.4_6[3]"), default false.

  :tx-margin         The length of transcription margin, up to a maximum of
                     10000, default 5000.

  :verbose?          Print debug information, default false.
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vcf-variant->hgvs
multimethod
(vcf-variant->hgvs variant ref-seq ref-gene)(vcf-variant->hgvs variant ref-seq ref-gene options)
Converts a VCF-style variant (:chr, :pos, :ref, and :alt) into HGVS. alt must
be a single alternation such as "TG". "TG,T", for example, is not allowed.
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 maps, each having :coding-dna and :protein HGVS defined in
clj-hgvs.

Options:

  :prefer-deletion?  Prefer deletion (e.g. "c.7_9del") to repeated
                     sequences (e.g. "c.4_6[1]"), default false.

  :prefer-insertion? Prefer insertion (e.g. "c.9_10insAGG") to repeated
                     sequences (e.g. "c.4_6[3]"), default false.

  :tx-margin         The length of transcription margin, up to a maximum of
                     10000, default 5000.

  :verbose?          Print debug information, default false.
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vcf-variant->protein-hgvs
multimethod
(vcf-variant->protein-hgvs variant ref-seq ref-gene)(vcf-variant->protein-hgvs variant ref-seq ref-gene options)
Converts a VCF-style variant (:chr, :pos, :ref, and :alt) into protein HGVS.
alt must be a single alternation such as "TG". "TG,T", for example, is not
allowed. 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 protein HGVS defined in clj-hgvs.

Options:

  :prefer-deletion?  Prefer deletion (e.g. "p.P7_H8del") to repeated
                     sequences (e.g. "p.P5_H6[1]"), default false.

  :prefer-insertion? Prefer insertion (e.g. "c.H9_L10insRPH") to repeated
                     sequences (e.g. "c.R4_H6[3]"), default false.

  :verbose?          Print debug information, default false.
view source