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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. AWS Credentials
  36. AWS Resources
  37. Abecasis Group Awards
  38. Abecasis Lab
  39. Alan Kwong
  40. Amazon Single Node
  41. Amazon Snapshot
  42. Amazon Storage
  43. An example of using libcsg
  44. Analyses of Indels
  45. Ancestry
  46. Ann Arbor Travel Basics
  47. Arf
  48. BAFRegress
  49. BAM
  50. BAM Review Action Items
  51. BAM to FASTQ
  52. BamGenotypeCheck
  53. BamPileup
  54. BamUtil
  55. BamUtil: FAQ
  56. BamUtil: asp
  57. BamUtil: bam2FastQ
  58. BamUtil: clipOverlap
  59. BamUtil: convert
  60. BamUtil: dedup
  61. BamUtil: diff
  62. BamUtil: dumpAsp
  63. BamUtil: dumpHeader
  64. BamUtil: dumpIndex
  65. BamUtil: dumpRefInfo
  66. BamUtil: explainFlags
  67. BamUtil: filter
  68. BamUtil: findCigars
  69. BamUtil: gapInfo
  70. BamUtil: indelDiscordance
  71. BamUtil: mergeBam
  72. BamUtil: polishBam
  73. BamUtil: readIndexedBam
  74. BamUtil: readReference
  75. BamUtil: recab
  76. BamUtil: revert
  77. BamUtil: splitBam
  78. BamUtil: splitChromosome
  79. BamUtil: squeeze
  80. BamUtil: stats
  81. BamUtil: trimBam
  82. BamUtil: validate
  83. BamUtil: writeRegion
  84. Bam read count
  85. Bar Harbor Statistical Genetics Workshop
  86. BaseQualityCheck
  87. Base Caller Summaries
  88. Basic Linux Intro
  89. Bayesdenovo
  90. Ben Lerch
  91. Better X Sessions from Home (NX)
  92. Biostatistics 501: Main Page
  93. Biostatistics 602: Main Page
  94. Biostatistics 615/815: Main Page
  95. Biostatistics 615/815 Fall 2011
  96. Biostatistics 615/815 Winter 2011
  97. Biostatistics 666: Advanced Coalescent, Changing Population Size
  98. Biostatistics 666: Advanced Coalescent, Computation with the Coalescent
  99. Biostatistics 666: Advanced Haplotype Estimation
  100. Biostatistics 666: Analysis of Copy Number Using Sequence Data
  101. Biostatistics 666: Analysis of Low Pass Sequence Data
  102. Biostatistics 666: Applications of the Lander-Green Algorithm
  103. Biostatistics 666: Association Tests in Structured Populations
  104. Biostatistics 666: Contemporary Human Genetics
  105. Biostatistics 666: Copy Number Variation
  106. Biostatistics 666: Core Competencies
  107. Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium
  108. Biostatistics 666: Genotype Imputation
  109. Biostatistics 666: Haplotype Association Tests
  110. Biostatistics 666: Haplotype Estimation
  111. Biostatistics 666: Hardy-Weinberg Equilibrium
  112. Biostatistics 666: Introduction to De Novo Assembly
  113. Biostatistics 666: Introduction to the Coalescent
  114. Biostatistics 666: Introduction to the E-M Algorithm
  115. Biostatistics 666: Introductory Lecture
  116. Biostatistics 666: Likelihood Calculations for Large Pedigrees
  117. Biostatistics 666: Linkage Analysis in Sibling Pairs
  118. Biostatistics 666: Linkage Disequilibrium
  119. Biostatistics 666: Linkage Tests for Pairs of Individuals
  120. Biostatistics 666: Main Page
  121. Biostatistics 666: Maximum Likelihood Allele Frequency Estimation
  122. Biostatistics 666: Modeling Recombination and Migration in the Coalescent
  123. Biostatistics 666: Modeling Variation in the Coalescent
  124. Biostatistics 666: Multipoint Analysis in Sibling Pairs
  125. Biostatistics 666: Power of Genomewide Association Studies
  126. Biostatistics 666: Rare Variant Burden Tests
  127. Biostatistics 666: Relationship Checking
  128. Biostatistics 666: The Lander-Green Algorithm
  129. Biostatistics 666: The Possible Triangle Constraint
  130. Biostatistics 666: Variance Component Analyses
  131. Biostatistics 666: Whole Genome Sequencing
  132. Biostatistics 815 Term Project
  133. Biostatistics 830: Core Competencies
  134. Biostatistics 830: Fall 2013 Edition
  135. Biostatistics 830: Main Page
  136. Biostatistics 830 - Code Snippets
  137. Biostatistics 866: Core Competencies
  138. Biostatistics 866: Main Page
  139. C++ Class: CigarRoller
  140. C++ Class: FastQFile
  141. C++ Class: InputFile
  142. C++ Class: Pedigree Example
  143. C++ Class: SamFile
  144. C++ Class: SamFileHeader
  145. C++ Class: SamRecord
  146. C++ Class Averages
  147. C++ Library: FASTQ Change Log
  148. C++ Library: general Change Log
  149. C++ Library: libStatGen
  150. CHARGE
  151. CSG Tech Talks
  152. CalcMatch
  153. CheckVCF.py
  154. ChunkChromosome
  155. CigarRoller Proposed Update
  156. Class Notes
  157. Code Sample: Generating Manhattan Plots in R
  158. Code Sample: Generating QQ Plots in R
  159. Computer How-Tos
  160. Configure GotCloud
  161. ContaminationDetection
  162. Creating a Snapshot on EC2
  163. Creating an AMI on EC2
  164. Dajiang Liu
  165. Debuggers
  166. DosageConvertor
  167. Dosage convertor
  168. EMADS
  169. EMADS Primary Analysis Plan
  170. EMMAX
  171. EPACTS
  172. EPACTS for DIAGRAM
  173. Editing Sequence Analysis Practice 2011/03/10
  174. Evaluating a Read Mapper on Simulated Data
  175. Example
  176. Examples of Read Mapping with Karma and BWA
  177. ExomePicks
  178. Exome Chip Design
  179. FASTA
  180. FTEC
  181. FamLDCaller
  182. FamRvTest command
  183. FamRvTest tutorial
  184. Famrvtest
  185. FastQValidator
  186. FastQ Validation Criteria
  187. Fst
  188. GBR60vc.conf
  189. GLF
  190. GREGOR
  191. GTDT
  192. GWAS
  193. Garlic
  194. Gene Ontology
  195. Generic Exome Analysis Plan
  196. Genezoom
  197. Genotype Likelihood Based Allele Balance
  198. Genotype Likelihood based Allele Frequency
  199. Genotype Likelihood based Hardy-Weinberg Test
  200. Genotype Likelihood based Inbreeding Coefficient
  201. Git Cheat Sheet
  202. Git FAQs
  203. GlfMerge
  204. GlfMultiples
  205. GlfSingle
  206. GlfTrio
  207. Goncalo Abecasis
  208. Goncalo Abecasis: Interview with Christiana Fogg
  209. GotCloud
  210. GotCloud: AMIs
  211. GotCloud: Alignment Pipeline
  212. GotCloud: Alignment Sub-Pipelines
  213. GotCloud: Amazon
  214. GotCloud: Amazon Demo
  215. GotCloud: Binary Releases
  216. GotCloud: Configuration
  217. GotCloud: Creating a New Pipeline
  218. GotCloud: FAQs
  219. GotCloud: Filters
  220. GotCloud: Genetic Reference and Resource Files
  221. GotCloud: GenomeSTRiP Pipeline
  222. GotCloud: RedHat Package
  223. GotCloud: Reference Files
  224. GotCloud: Source Releases
  225. GotCloud: Variant Calling Options
  226. GotCloud: Variant Calling Pipeline
  227. GotCloud: Versions
  228. Gzip
  229. Gzip File
  230. HAPMIX
  231. Haploxt
  232. Hardy Weinberg equilibrium
  233. How To Use Git
  234. How to use aspera
  235. IGFPipe
  236. IMPUTE2
  237. IMPUTE2: 1000 Genomes Imputation Cookbook
  238. Idriver
  239. Imputation Server: Example
  240. Indel
  241. Installing MinGW & MSYS on Windows
  242. Introduction to new students
  243. Jennifer Bragg-Gresham
  244. Karma
  245. Karma-colorspace
  246. Kyoto Encyclopedia of Genes and Genomes
  247. LASER
  248. Lars Fritsche
  249. LibStatGen: ASP
  250. LibStatGen: BAM

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