Biostatistics 830 - Code Snippets

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::Transpose()

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::WalkLeft()

830 - MarkovModel::WalkRight()

830 - MarkovModel::Impute()

830 - MarkovModel::CountRecombinants()

830 - MarkovModel::CountErrors()

830 - MarkovModel::CountErrorsAndRecombinants()

830 - MINIMAC::main()

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 - BasicMapper::main()

830 - MaqIndex::GetWord()

830 - MaqIndex::BuildIndex()

830 - MaqIndex::LookupWord()

830 - MaqIndex::CompareToIndex()

830 - BestAlignment::MaqAlignment()

830 - BestAlignment::EvaluateAlignment() (main loop)

830 - BestAlignment::EvaluateAlignment() (detailed comparison)

830 - BestAlignment::isNewPosition()

830 - BestAlignment::IterateCache()

830 - BestAlignment::ClearPositions()