bio-sam-mutation

Methods for calling mutations from SAM alignments, including CIGAR and MD tag parsers.
Annotates mutations in HGVS format: http://www.hgvs.org/mutnomen/recs.html.
Incorporates Ensembl VEP lookup.

Installation

gem install bio-sam-mutation

Usage

require 'bio-sam-mutation'

  # NB must be tab-delimited
  insertion_and_deletion = Bio::DB::Alignment.new("I2M5K:00253:00406\t0\t5\t112839854\t70\t63M2I138M1D27M7S\t*\t0\t0\tCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCATACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTATTACATTTTGCCACGGAAAGTACTGCTGAGG\t@CDDDCCCCACACCCCCCCC?CCACCCC>A6;;;;7;;6;6;BC;;6;;;;;.;;>ADDA??;;;;;?CCACCCD>C??@CCCC>C@C;>?CCCC@C=::@:::::+:::/:CCC?>>>>CCCCDDD9CCCC@AB????=AB>??;?BB>@@@AA???CC<@@?????BB>??;;;B<BC;??8;6:A=@=@BBB;;;?<77//*08*088888*8=9=?B7;;4;??????????<\tPG:Z:novoalign\tAS:i:183\tUQ:i:183\tNM:i:3\tMD:Z:201^T27")

  insertion_and_deletion.mutations
  #=> [#<Bio::Mutation:0x007fa20b5b4fc8 @position=112839916, @type=:insertion, @reference=nil, @mutant="AT", @seqname="5">, #<Bio::Mutation:0x007fa20b5b4960 @position=112840055, @type=:deletion, @reference="T", @mutant=nil, @seqname="5">]

  insertion_and_deletion.mutations.first.to_hgvs("g")
  #=> "5:g.112839916_112839917insAT"

  puts YAML.dump(insertion_and_deletion.mutations.first.vep("human","g").first["transcript_consequences"].keep_if{|c| c["transcript_id"] == "ENST00000257430"})
  #---
  # - variant_allele: AT
  #   cdna_end: 4379
  #   codons: cca/ccATa
  #   protein_end: 1441
  #   strand: 1
  #   hgnc_id: HGNC:583
  #   amino_acids: P/PX
  #   gene_symbol: APC
  #   cdna_start: 4378
  #   transcript_id: ENST00000257430
  #   cds_start: 4322
  #   gene_id: ENSG00000134982
  #   protein_start: 1441
  #   biotype: protein_coding
  #   gene_symbol_source: HGNC
  #   cds_end: 4323
  #   consequence_terms:
  #   - frameshift_variant
  #   impact: HIGH
  # => nil

# E.g. of full request return
# http://rest.ensembl.org/documentation/info/vep_hgvs_get
insertion_and_deletion.mutations(112839854).first.vep("human","g")
# => [{"assembly_name"=>"GRCh38", "end"=>112839917, "seq_region_name"=>"5", "transcript_consequences"=>[{"gene_id"=>"ENSG00000134982", "distance"=>46, "variant_allele"=>"AT", "biotype"=>"nonsense_mediated_decay", "gene_symbol_source"=>"HGNC", "consequence_terms"=>["downstream_gene_variant"], "strand"=>1, "hgnc_id"=>"HGNC:583", "gene_symbol"=>"APC", "transcript_id"=>"ENST00000502371", "impact"=>"MODIFIER"}, {"variant_allele"=>"AT", "cdna_end"=>4380, "codons"=>"-/AT", "protein_end"=>1442, "strand"=>1, "hgnc_id"=>"HGNC:583", "amino_acids"=>"-/X", "gene_symbol"=>"APC", "cdna_start"=>4379, "transcript_id"=>"ENST00000257430", "cds_start"=>4323, "gene_id"=>"ENSG00000134982", "protein_start"=>1441, "biotype"=>"protein_coding", "gene_symbol_source"=>"HGNC", "cds_end"=>4324, "consequence_terms"=>["frameshift_variant"], "impact"=>"HIGH"}, {"gene_id"=>"ENSG00000134982", "distance"=>863, "variant_allele"=>"AT", "biotype"=>"protein_coding", "gene_symbol_source"=>"HGNC", "consequence_terms"=>["downstream_gene_variant"], "strand"=>1, "hgnc_id"=>"HGNC:583", "gene_symbol"=>"APC", "transcript_id"=>"ENST00000507379", "impact"=>"MODIFIER"}, {"variant_allele"=>"AT", "cdna_end"=>4481, "codons"=>"-/AT", "protein_end"=>1442, "strand"=>1, "hgnc_id"=>"HGNC:583", "amino_acids"=>"-/X", "gene_symbol"=>"APC", "cdna_start"=>4480, "transcript_id"=>"ENST00000508376", "cds_start"=>4323, "gene_id"=>"ENSG00000134982", "protein_start"=>1441, "biotype"=>"protein_coding", "gene_symbol_source"=>"HGNC", "cds_end"=>4324, "consequence_terms"=>["frameshift_variant"], "impact"=>"HIGH"}, {"gene_id"=>"ENSG00000134982", "distance"=>409, "variant_allele"=>"AT", "biotype"=>"protein_coding", "gene_symbol_source"=>"HGNC", "consequence_terms"=>["downstream_gene_variant"], "strand"=>1, "hgnc_id"=>"HGNC:583", "gene_symbol"=>"APC", "transcript_id"=>"ENST00000512211", "impact"=>"MODIFIER"}, {"gene_id"=>"ENSG00000134982", "variant_allele"=>"AT", "cdna_end"=>4569, "biotype"=>"nonsense_mediated_decay", "gene_symbol_source"=>"HGNC", "consequence_terms"=>["3_prime_UTR_variant", "NMD_transcript_variant"], "strand"=>1, "hgnc_id"=>"HGNC:583", "gene_symbol"=>"APC", "cdna_start"=>4568, "transcript_id"=>"ENST00000508624", "impact"=>"MODIFIER"}, {"gene_id"=>"ENSG00000258864", "variant_allele"=>"AT", "biotype"=>"nonsense_mediated_decay", "gene_symbol_source"=>"Clone_based_vega_gene", "consequence_terms"=>["intron_variant", "NMD_transcript_variant"], "strand"=>1, "gene_symbol"=>"CTC-554D6.1", "transcript_id"=>"ENST00000520401", "impact"=>"MODIFIER"}, {"gene_id"=>"ENSG00000134982", "distance"=>2195, "variant_allele"=>"AT", "biotype"=>"protein_coding", "gene_symbol_source"=>"HGNC", "consequence_terms"=>["downstream_gene_variant"], "strand"=>1, "hgnc_id"=>"HGNC:583", "gene_symbol"=>"APC", "transcript_id"=>"ENST00000504915", "impact"=>"MODIFIER"}], "strand"=>1, "id"=>"5:g.112839917_112839918insAT", "allele_string"=>"-/AT", "most_severe_consequence"=>"frameshift_variant", "start"=>112839918}]

The API doc is online. For more code examples see the test files in the source tree.

Project home page

Information on the source tree, documentation, examples, issues and how to contribute, see

http://github.com/stveep/bioruby-sam-mutation

The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.

Cite

If you use this software, please cite one of

Biogems.info