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Revision as of 13:53, 28 October 2013
, 13:53, 28 October 2013→Code Snippets
[[830 - Haplotyper::ConditionOnData()]]
[[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()]]
