Difference between revisions of "Biostatistics 830 - Code Snippets"
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+ | [[830 - BestAlignment::EvaluateAlignment() (main loop)]] | ||
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+ | [[830 - BestAlignment::EvaluateAlignment() (detailed comparison)]] |
Revision as of 13:44, 28 October 2013
Li et al (2010) Genet Epidemiol
Full Citation
Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol. 34:816-34
Code Snippets
830 - Haplotyper::RandomSetup()
830 - Haplotyper::SetupPrior()
830 - Haplotyper::ConditionOnData()
830 - Haplotyper::ScoreLeftConditional()
830 - Haplotyper::ScoreLeftConditional() (smart, complicated)
830 - Haplotyper::SampleChromosomes()
830 - Haplotyper::SampleHaplotypes()
830 - Haplotyper::SummarizeOptions()
830 - Haplotyper::SampleOneHaplotype()
830 - Haplotyper::ImputeGenotypes()
830 - Haplotyper::ImputeGenotypes() (edge)
830 - Haplotyper::ImputeGenotypes() (internal)
Howie et al (2012) Nat Genet
Full Citation
Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet. 44:955-9. PMID: 22820512
Code Snippets
830 - MarkovModel::Transpose()
830 - MarkovModel::Condition()
830 - MarkovModel::WalkRight()
830 - MarkovModel::CountRecombinants()
830 - MarkovModel::CountErrors()
830 - MarkovModel::CountErrorsAndRecombinants()
Li et al (2013) Genome Research
Full Citation
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18:1851-8.
Code Snippets
830 - MaqIndex::CompareToIndex()
830 - BestAlignment::MaqAlignment()
830 - BestAlignment::EvaluateAlignment() (main loop)
830 - BestAlignment::EvaluateAlignment() (detailed comparison)