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  1. 1000 Genomes Project Pilot 1 SNP Calling
  2. 830 - BasicMapper::main()
  3. 830 - BestAlignment::ClearPositions()
  4. 830 - BestAlignment::EvaluateAlignment() (detailed comparison)
  5. 830 - BestAlignment::EvaluateAlignment() (main loop)
  6. 830 - BestAlignment::IterateCache()
  7. 830 - BestAlignment::MaqAlignment()
  8. 830 - BestAlignment::isNewPosition()
  9. 830 - Haplotyper::ConditionOnData()
  10. 830 - Haplotyper::ImputeGenotypes()
  11. 830 - Haplotyper::ImputeGenotypes() (edge)
  12. 830 - Haplotyper::ImputeGenotypes() (internal)
  13. 830 - Haplotyper::RandomSetup()
  14. 830 - Haplotyper::SampleChromosomes()
  15. 830 - Haplotyper::SampleHaplotypes()
  16. 830 - Haplotyper::SampleOneHaplotype()
  17. 830 - Haplotyper::ScoreLeftConditional()
  18. 830 - Haplotyper::ScoreLeftConditional() (smart, complicated)
  19. 830 - Haplotyper::SetupPrior()
  20. 830 - Haplotyper::SummarizeOptions()
  21. 830 - Haplotyper::Transpose()
  22. 830 - MINIMAC::main()
  23. 830 - MaqIndex::BuildIndex()
  24. 830 - MaqIndex::CompareToIndex()
  25. 830 - MaqIndex::GetWord()
  26. 830 - MaqIndex::LookupWord()
  27. 830 - MarkovModel::Condition()
  28. 830 - MarkovModel::CountErrors()
  29. 830 - MarkovModel::CountErrorsAndRecombinants()
  30. 830 - MarkovModel::CountRecombinants()
  31. 830 - MarkovModel::Impute()
  32. 830 - MarkovModel::Transpose()
  33. 830 - MarkovModel::WalkLeft()
  34. 830 - MarkovModel::WalkRight()
  35. Abecasis Group Awards
  36. An example of using libcsg
  37. Ancestry
  38. Ann Arbor Travel Basics
  39. BAFRegress
  40. BAM Review Action Items
  41. BamPileup
  42. Bam read count
  43. BaseQualityCheck
  44. Base Caller Summaries
  45. Basic Linux Intro
  46. Bayesdenovo
  47. Better X Sessions from Home (NX)
  48. Biostatistics 602: Main Page
  49. Biostatistics 666: Advanced Coalescent, Changing Population Size
  50. Biostatistics 666: Advanced Coalescent, Computation with the Coalescent
  51. Biostatistics 666: Advanced Haplotype Estimation
  52. Biostatistics 666: Analysis of Copy Number Using Sequence Data
  53. Biostatistics 666: Analysis of Low Pass Sequence Data
  54. Biostatistics 666: Applications of the Lander-Green Algorithm
  55. Biostatistics 666: Association Tests in Structured Populations
  56. Biostatistics 666: Contemporary Human Genetics
  57. Biostatistics 666: Copy Number Variation
  58. Biostatistics 666: Genotype Imputation
  59. Biostatistics 666: Haplotype Association Tests
  60. Biostatistics 666: Haplotype Estimation
  61. Biostatistics 666: Hardy-Weinberg Equilibrium
  62. Biostatistics 666: Introduction to De Novo Assembly
  63. Biostatistics 666: Introduction to the Coalescent
  64. Biostatistics 666: Introduction to the E-M Algorithm
  65. Biostatistics 666: Introductory Lecture
  66. Biostatistics 666: Likelihood Calculations for Large Pedigrees
  67. Biostatistics 666: Linkage Analysis in Sibling Pairs
  68. Biostatistics 666: Linkage Disequilibrium
  69. Biostatistics 666: Linkage Tests for Pairs of Individuals
  70. Biostatistics 666: Maximum Likelihood Allele Frequency Estimation
  71. Biostatistics 666: Modeling Recombination and Migration in the Coalescent
  72. Biostatistics 666: Modeling Variation in the Coalescent
  73. Biostatistics 666: Multipoint Analysis in Sibling Pairs
  74. Biostatistics 666: Rare Variant Burden Tests
  75. Biostatistics 666: Relationship Checking
  76. Biostatistics 666: The Lander-Green Algorithm
  77. Biostatistics 666: The Possible Triangle Constraint
  78. Biostatistics 666: Variance Component Analyses
  79. Biostatistics 666: Whole Genome Sequencing
  80. Biostatistics 815 Term Project
  81. C++ Class: InputFile
  82. C++ Class: Pedigree Example
  83. C++ Class Averages
  84. CHARGE
  85. CSG Tech Talks
  86. CalcMatch
  87. CheckVCF.py
  88. CigarRoller Proposed Update
  89. Code Sample: Generating Manhattan Plots in R
  90. Code Sample: Generating QQ Plots in R
  91. Dosage convertor
  92. Editing Sequence Analysis Practice 2011/03/10
  93. Evaluating a Read Mapper on Simulated Data
  94. Example
  95. Examples of Read Mapping with Karma and BWA
  96. ExomePicks
  97. FASTA
  98. FamRvTest tutorial
  99. Fst
  100. GREGOR

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