Line 8: |
Line 8: |
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| [[830 - Haplotyper::RandomSetup()]] | | [[830 - Haplotyper::RandomSetup()]] |
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| + | [[830 - Haplotyper::SetupPrior()]] |
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| [[830 - Haplotyper::Transpose()]] | | [[830 - Haplotyper::Transpose()]] |
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| + | [[830 - Haplotyper::ConditionOnData()]] |
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| + | [[830 - Haplotyper::ScoreLeftConditional()]] |
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| + | [[830 - Haplotyper::ScoreLeftConditional() (smart, complicated)]] |
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| + | [[830 - Haplotyper::SampleChromosomes()]] |
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| + | [[830 - Haplotyper::SampleHaplotypes()]] |
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| + | [[830 - Haplotyper::SummarizeOptions()]] |
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| + | [[830 - Haplotyper::SampleOneHaplotype()]] |
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| + | [[830 - Haplotyper::ImputeGenotypes()]] |
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| + | [[830 - Haplotyper::ImputeGenotypes() (edge)]] |
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| + | [[830 - Haplotyper::ImputeGenotypes() (internal)]] |
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| + | == Howie et al (2012) Nat Genet == |
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| + | === Full Citation === |
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| + | 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 |
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| + | === Code Snippets === |
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| + | [[830 - MarkovModel::Transpose()]] |
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| + | [[830 - MarkovModel::Condition()]] |
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| + | [[830 - MarkovModel::WalkLeft()]] |
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| + | [[830 - MarkovModel::WalkRight()]] |
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| + | [[830 - MarkovModel::Impute()]] |
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| + | [[830 - MarkovModel::CountRecombinants()]] |
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| + | [[830 - MarkovModel::CountErrors()]] |
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| + | [[830 - MarkovModel::CountErrorsAndRecombinants()]] |
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| + | [[830 - MINIMAC::main()]] |
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| + | == Li et al (2013) Genome Research == |
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| + | === Full Citation === |
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| + | Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. ''Genome Res.'' '''18''':1851-8. |
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| + | === Code Snippets === |
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| + | [[830 - BasicMapper::main()]] |
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| + | [[830 - MaqIndex::GetWord()]] |
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| + | [[830 - MaqIndex::BuildIndex()]] |
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| + | [[830 - MaqIndex::LookupWord()]] |
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| + | [[830 - MaqIndex::CompareToIndex()]] |
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| + | [[830 - BestAlignment::MaqAlignment()]] |
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| + | [[830 - BestAlignment::EvaluateAlignment() (main loop)]] |
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| + | [[830 - BestAlignment::EvaluateAlignment() (detailed comparison)]] |
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| + | [[830 - BestAlignment::isNewPosition()]] |
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| + | [[830 - BestAlignment::IterateCache()]] |
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| + | [[830 - BestAlignment::ClearPositions()]] |