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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
  251. LibStatGen: FASTQ
  252. LibStatGen: GLF
  253. LibStatGen: VCF
  254. LibStatGen: general
  255. LibStatGen Download
  256. LibStatGen Repository
  257. LibStatGen Troubleshooting
  258. LiftMap.py
  259. LiftOver
  260. LiftRsNumber.py
  261. Ligate Minimac
  262. Links to Sequence Analysis Tools
  263. LocusZoom
  264. LocusZoom Standalone
  265. M3VCF Files
  266. M3vcftools
  267. M3vcftools Usage
  268. MEAGA
  269. MERLIN format
  270. METAL
  271. METAL ADDFILTER
  272. METAL COLUMNCOUNTING
  273. METAL CUSTOMVARIABLE
  274. METAL Command Reference
  275. METAL Documentation
  276. METAL EFFECTLABEL
  277. METAL FAQ
  278. METAL GENOMICCONTROL
  279. METAL Glucose Example Script
  280. METAL LOGPVALUE
  281. METAL Quick Start
  282. METAL SOURCE
  283. METAL VERBOSE
  284. MaCH
  285. MaCH: 1000 Genomes Imputation Cookbook
  286. MaCH: Input Files
  287. MaCH: Pedigree with Integer Allele Codes
  288. MaCH: machX
  289. MaCH FAQ
  290. MaCH Options
  291. Mach2dat: Association with MACH output
  292. Mach DAC
  293. Main Page
  294. Make file tutorial
  295. Makefile.tool
  296. Mantra.cpp
  297. MappabilityScores
  298. Mapping Quality Scores
  299. Mary Kate Wing
  300. Merlin
  301. MetaMinimac
  302. Meta Analysis of SNPxEnvironment Interaction
  303. Minimac
  304. Minimac2
  305. Minimac3
  306. Minimac3 - Full List of Options
  307. Minimac3 ChangeLog
  308. Minimac3 Cookbook : Chromosome X Imputation
  309. Minimac3 Cookbook : Converting Files to VCF
  310. Minimac3 Cookbook : Pre-Phasing
  311. Minimac3 Examples
  312. Minimac3 Imputation Cookbook
  313. Minimac3 Info (Older Version)
  314. Minimac3 Info File
  315. Minimac3 Usage
  316. Minimac4
  317. Minimac4 - Full List of Options
  318. Minimac4 Documentation
  319. Minimac: 1000 Genomes Imputation Cookbook
  320. Minimac: Tutorial
  321. Minimac Command Reference
  322. Minimac Diagnostics
  323. Mount S3 Volume
  324. MutationFilter
  325. NHLBI Exome Sequencing Project
  326. NHLBI Informatics Resource
  327. New Fugue
  328. Outcomes For Mapping A Paired End
  329. Parameters.h
  330. PedScript
  331. PhoneHome
  332. Phred scale
  333. Pileup
  334. PileupBasedVariantCalling
  335. Polymutt
  336. Polymutt2
  337. Polymutt beta
  338. Power Calculations: Quantitative Traits
  339. QPLOT
  340. RAREFY
  341. RAREFY COMMAND
  342. RAREFY DOCUMENTATION
  343. RAREFY DOWNLOAD
  344. RAREFY FAQ
  345. RAREFY TUTORIAL
  346. RAREMETAL
  347. RAREMETALWORKER
  348. RAREMETALWORKER METHOD
  349. RAREMETALWORKER SPECIAL TOPICS
  350. RAREMETALWORKER X
  351. RAREMETALWORKER command reference
  352. RAREMETAL Change Log
  353. RAREMETAL Command Reference
  354. RAREMETAL DOWNLOAD & BUILD
  355. RAREMETAL Documentation
  356. RAREMETAL FAQ
  357. RAREMETAL METHOD
  358. Rare-metal-worker
  359. RareMETALS
  360. RareMETALS2
  361. RareMetals
  362. RareSimu
  363. Rare Variant Analysis and Meta-Analysis
  364. Rare variant tests
  365. Raremetal Incoming updates
  366. Read Mapping
  367. Regions of high linkage disequilibrium (LD)
  368. Relationship between Ploidy, Alleles and Genotypes
  369. RelativeFinder
  370. Releasing GotCloud
  371. RvTests
  372. Rvtests
  373. SAM
  374. SAM/BAM Classes FAQs
  375. SAM/BAM Convert Sequence
  376. SAM: Filtering Reads
  377. SAM Validation Criteria
  378. SAV Command Line Interface
  379. SAV File Format
  380. SEQMIX
  381. SNP Call Set Properties
  382. Sam Library Usage Examples
  383. Samtools-hybrid
  384. Sara Rashkin
  385. SardiNIA
  386. SardiNIA project meeting July 15-16, 2013
  387. SavR
  388. Savvy C++ Library
  389. Sayantan Das
  390. Scott Vrieze
  391. Screen Commands
  392. Sean Caron
  393. SeqShop: Aligning Your Own Genome, December 2014
  394. SeqShop: Aligning Your Own Genome, June 2014
  395. SeqShop: Aligning Your Own Genome, May 2015
  396. SeqShop: Analysis of Structural Variation Practical, December 2014
  397. SeqShop: Analysis of Structural Variation Practical, June 2014
  398. SeqShop: Analysis of Structural Variation Practical, May 2015
  399. SeqShop: Ancestry On Your Own Genome, December 2014
  400. SeqShop: Ancestry On Your Own Genome, June 2014
  401. SeqShop: Ancestry On Your Own Genome, May 2015
  402. SeqShop: Association Analysis, May 2015
  403. SeqShop: Calling Your Own Genome, December 2014
  404. SeqShop: Calling Your Own Genome, June 2014
  405. SeqShop: Calling Your Own Genome, May 2015
  406. SeqShop: December 2014
  407. SeqShop: Estimates of Genetic Ancestry Practical, December 2014
  408. SeqShop: Estimates of Genetic Ancestry Practical, June 2014
  409. SeqShop: Estimates of Genetic Ancestry Practical, May 2015
  410. SeqShop: Friday - Practicing what we learned, June 2014
  411. SeqShop: Genetic Association Analysis Practical, December 2014
  412. SeqShop: Genetic Association Analysis Practical, June 2014
  413. SeqShop: June 2014
  414. SeqShop: May 2015
  415. SeqShop: Sequence Mapping and Assembly Practical, December 2014
  416. SeqShop: Sequence Mapping and Assembly Practical, June 2014
  417. SeqShop: Sequence Mapping and Assembly Practical, May 2015
  418. SeqShop: Variant Calling and Filtering for INDELs Practical, December 2014
  419. SeqShop: Variant Calling and Filtering for INDELs Practical, June 2014
  420. SeqShop: Variant Calling and Filtering for INDELs Practical, May 2015
  421. SeqShop: Variant Calling and Filtering for SNPs Practical, December 2014
  422. SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014
  423. SeqShop: Variant Calling and Filtering for SNPs Practical, May 2015
  424. Sequence Analysis Practice 2011/03/09
  425. Sequencing Workshop Analysis of Indels
  426. Short Workshops
  427. Shuang Feng
  428. Software
  429. SplitPed
  430. SplitRef
  431. StarCluster
  432. StatgenTools
  433. StatsTools
  434. Stouffer Method for Meta-Analysis
  435. StringMap.h
  436. Summary Statistics Files Specification for RAREMETAL and rvtests
  437. TOPMed Site Visit 2018
  438. TabAnno
  439. Tandem Repeat Concepts
  440. Test EPACTS for DIAGRAM
  441. Thunder
  442. ThunderVCF
  443. TinySimulator
  444. Tom Blackwell
  445. Tramp
  446. Trial Enrichment
  447. TrioCaller
  448. TrioCaller:Archive
  449. Triodenovo
  450. Tutorial: EMMAX GotCloud STOM
  451. Tutorial: EMMAX GotCloud STOM: Lecture 2
  452. Tutorial: EMMAX GotCloud STOM: Lecture 5
  453. Tutorial: EMMAX GotCloud STOM: Lecture 6
  454. Tutorial: EMMAX GotCloud STOM: Lecture 8
  455. Tutorial: GotCloud
  456. Tutorial: GotCloud UW CMG
  457. Tutorial: Low Pass Sequence Analysis
  458. Tutorial: Low Pass Sequence Analysis Answers
  459. Tutorial: RAREMETAL
  460. UMAKE
  461. UMAKE-glfSingle
  462. Understanding QPLOT output
  463. Understanding VerifyBamID output
  464. Understanding vcf-summary output
  465. Using Git Example
  466. Using Gotcloud on Flux
  467. Utility Library
  468. VCF
  469. VICES
  470. Variant Call Pipeline
  471. Variant Normalization
  472. Variant classification
  473. Vcf2geno
  474. VcfCodingSnps
  475. VcfCooker
  476. VcfGenomeStat
  477. VcfRefGen
  478. VerifyBamID
  479. VerifyIDintensity
  480. Verifying Sample Identities - Implementation
  481. Vmatch
  482. Vpeep
  483. Vt
  484. Xiaowei Zhan
  485. Zlib

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