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- 830 - BasicMapper::main()
- 830 - BestAlignment::ClearPositions()
- 830 - BestAlignment::EvaluateAlignment() (detailed comparison)
- 830 - BestAlignment::EvaluateAlignment() (main loop)
- 830 - BestAlignment::IterateCache()
- 830 - BestAlignment::MaqAlignment()
- 830 - BestAlignment::isNewPosition()
- 830 - Haplotyper::ConditionOnData()
- 830 - Haplotyper::ImputeGenotypes()
- 830 - Haplotyper::ImputeGenotypes() (edge)
- 830 - Haplotyper::ImputeGenotypes() (internal)
- 830 - Haplotyper::RandomSetup()
- 830 - Haplotyper::SampleChromosomes()
- 830 - Haplotyper::SampleHaplotypes()
- 830 - Haplotyper::SampleOneHaplotype()
- 830 - Haplotyper::ScoreLeftConditional()
- 830 - Haplotyper::ScoreLeftConditional() (smart, complicated)
- 830 - Haplotyper::SetupPrior()
- 830 - Haplotyper::SummarizeOptions()
- 830 - Haplotyper::Transpose()
- 830 - MINIMAC::main()
- 830 - MaqIndex::BuildIndex()
- 830 - MaqIndex::CompareToIndex()
- 830 - MaqIndex::GetWord()
- 830 - MaqIndex::LookupWord()
- 830 - MarkovModel::Condition()
- 830 - MarkovModel::CountErrors()
- 830 - MarkovModel::CountErrorsAndRecombinants()
- 830 - MarkovModel::CountRecombinants()
- 830 - MarkovModel::Impute()
- 830 - MarkovModel::Transpose()
- 830 - MarkovModel::WalkLeft()
- 830 - MarkovModel::WalkRight()
- AWS Credentials
- AWS Resources
- Abecasis Group Awards
- Abecasis Lab
- Alan Kwong
- Amazon Single Node
- Amazon Snapshot
- Amazon Storage
- An example of using libcsg
- Analyses of Indels
- Ancestry
- Ann Arbor Travel Basics
- Arf
- BAFRegress
- BAM
- BAM Review Action Items
- BAM to FASTQ
- BamGenotypeCheck
- BamPileup
- BamUtil
- BamUtil: FAQ
- BamUtil: asp
- BamUtil: bam2FastQ
- BamUtil: clipOverlap
- BamUtil: convert
- BamUtil: dedup
- BamUtil: diff
- BamUtil: dumpAsp
- BamUtil: dumpHeader
- BamUtil: dumpIndex
- BamUtil: dumpRefInfo
- BamUtil: explainFlags
- BamUtil: filter
- BamUtil: findCigars
- BamUtil: gapInfo
- BamUtil: indelDiscordance
- BamUtil: mergeBam
- BamUtil: polishBam
- BamUtil: readIndexedBam
- BamUtil: readReference
- BamUtil: recab
- BamUtil: revert
- BamUtil: splitBam
- BamUtil: splitChromosome
- BamUtil: squeeze
- BamUtil: stats
- BamUtil: trimBam
- BamUtil: validate
- BamUtil: writeRegion
- Bam read count
- Bar Harbor Statistical Genetics Workshop
- BaseQualityCheck
- Base Caller Summaries
- Basic Linux Intro
- Bayesdenovo
- Ben Lerch
- Better X Sessions from Home (NX)
- Biostatistics 501: Main Page
- Biostatistics 602: Main Page
- Biostatistics 615/815: Main Page
- Biostatistics 615/815 Fall 2011
- Biostatistics 615/815 Winter 2011
- Biostatistics 666: Advanced Coalescent, Changing Population Size
- Biostatistics 666: Advanced Coalescent, Computation with the Coalescent
- Biostatistics 666: Advanced Haplotype Estimation
- Biostatistics 666: Analysis of Copy Number Using Sequence Data
- Biostatistics 666: Analysis of Low Pass Sequence Data
- Biostatistics 666: Applications of the Lander-Green Algorithm
- Biostatistics 666: Association Tests in Structured Populations
- Biostatistics 666: Contemporary Human Genetics
- Biostatistics 666: Copy Number Variation
- Biostatistics 666: Core Competencies
- Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium
- Biostatistics 666: Genotype Imputation
- Biostatistics 666: Haplotype Association Tests
- Biostatistics 666: Haplotype Estimation
- Biostatistics 666: Hardy-Weinberg Equilibrium
- Biostatistics 666: Introduction to De Novo Assembly
- Biostatistics 666: Introduction to the Coalescent
- Biostatistics 666: Introduction to the E-M Algorithm
- Biostatistics 666: Introductory Lecture
- Biostatistics 666: Likelihood Calculations for Large Pedigrees
- Biostatistics 666: Linkage Analysis in Sibling Pairs
- Biostatistics 666: Linkage Disequilibrium
- Biostatistics 666: Linkage Tests for Pairs of Individuals
- Biostatistics 666: Main Page
- Biostatistics 666: Maximum Likelihood Allele Frequency Estimation
- Biostatistics 666: Modeling Recombination and Migration in the Coalescent
- Biostatistics 666: Modeling Variation in the Coalescent
- Biostatistics 666: Multipoint Analysis in Sibling Pairs
- Biostatistics 666: Power of Genomewide Association Studies
- Biostatistics 666: Rare Variant Burden Tests
- Biostatistics 666: Relationship Checking
- Biostatistics 666: The Lander-Green Algorithm
- Biostatistics 666: The Possible Triangle Constraint
- Biostatistics 666: Variance Component Analyses
- Biostatistics 666: Whole Genome Sequencing
- Biostatistics 815 Term Project
- Biostatistics 830: Core Competencies
- Biostatistics 830: Fall 2013 Edition
- Biostatistics 830: Main Page
- Biostatistics 830 - Code Snippets
- Biostatistics 866: Core Competencies
- Biostatistics 866: Main Page
- C++ Class: CigarRoller
- C++ Class: FastQFile
- C++ Class: InputFile
- C++ Class: Pedigree Example
- C++ Class: SamFile
- C++ Class: SamFileHeader
- C++ Class: SamRecord
- C++ Class Averages
- C++ Library: FASTQ Change Log
- C++ Library: general Change Log
- C++ Library: libStatGen
- CHARGE
- CSG Tech Talks
- CalcMatch
- CheckVCF.py
- ChunkChromosome
- CigarRoller Proposed Update
- Class Notes
- Code Sample: Generating Manhattan Plots in R
- Code Sample: Generating QQ Plots in R
- Computer How-Tos
- Configure GotCloud
- ContaminationDetection
- Creating a Snapshot on EC2
- Creating an AMI on EC2
- Dajiang Liu
- Debuggers
- DosageConvertor
- Dosage convertor
- EMADS
- EMADS Primary Analysis Plan
- EMMAX
- EPACTS
- EPACTS for DIAGRAM
- Editing Sequence Analysis Practice 2011/03/10
- Evaluating a Read Mapper on Simulated Data
- Example
- Examples of Read Mapping with Karma and BWA
- ExomePicks
- Exome Chip Design
- FASTA
- FTEC
- FamLDCaller
- FamRvTest command
- FamRvTest tutorial
- Famrvtest
- FastQValidator
- FastQ Validation Criteria
- Fst
- GBR60vc.conf
- GLF
- GREGOR
- GTDT
- GWAS
- Garlic
- Gene Ontology
- Generic Exome Analysis Plan
- Genezoom
- Genotype Likelihood Based Allele Balance
- Genotype Likelihood based Allele Frequency
- Genotype Likelihood based Hardy-Weinberg Test
- Genotype Likelihood based Inbreeding Coefficient
- Git Cheat Sheet
- Git FAQs
- GlfMerge
- GlfMultiples
- GlfSingle
- GlfTrio
- Goncalo Abecasis
- Goncalo Abecasis: Interview with Christiana Fogg
- GotCloud
- GotCloud: AMIs
- GotCloud: Alignment Pipeline
- GotCloud: Alignment Sub-Pipelines
- GotCloud: Amazon
- GotCloud: Amazon Demo
- GotCloud: Binary Releases
- GotCloud: Configuration
- GotCloud: Creating a New Pipeline
- GotCloud: FAQs
- GotCloud: Filters
- GotCloud: Genetic Reference and Resource Files
- GotCloud: GenomeSTRiP Pipeline
- GotCloud: RedHat Package
- GotCloud: Reference Files
- GotCloud: Source Releases
- GotCloud: Variant Calling Options
- GotCloud: Variant Calling Pipeline
- GotCloud: Versions
- Gzip
- Gzip File
- HAPMIX
- Haploxt
- Hardy Weinberg equilibrium
- How To Use Git
- How to use aspera
- IGFPipe
- IMPUTE2
- IMPUTE2: 1000 Genomes Imputation Cookbook
- Idriver
- Imputation Server: Example
- Indel
- Installing MinGW & MSYS on Windows
- Introduction to new students
- Jennifer Bragg-Gresham
- Karma
- Karma-colorspace
- Kyoto Encyclopedia of Genes and Genomes
- LASER
- Lars Fritsche
- LibStatGen: ASP
- LibStatGen: BAM
- LibStatGen: FASTQ
- LibStatGen: GLF
- LibStatGen: VCF
- LibStatGen: general
- LibStatGen Download
- LibStatGen Repository
- LibStatGen Troubleshooting
- LiftMap.py
- LiftOver
- LiftRsNumber.py
- Ligate Minimac
- Links to Sequence Analysis Tools
- LocusZoom
- LocusZoom Standalone
- M3VCF Files
- M3vcftools
- M3vcftools Usage
- MEAGA
- MERLIN format
- METAL
- METAL ADDFILTER
- METAL COLUMNCOUNTING
- METAL CUSTOMVARIABLE
- METAL Command Reference
- METAL Documentation
- METAL EFFECTLABEL
- METAL FAQ
- METAL GENOMICCONTROL
- METAL Glucose Example Script
- METAL LOGPVALUE
- METAL Quick Start
- METAL SOURCE
- METAL VERBOSE
- MaCH
- MaCH: 1000 Genomes Imputation Cookbook
- MaCH: Input Files
- MaCH: Pedigree with Integer Allele Codes
- MaCH: machX
- MaCH FAQ
- MaCH Options
- Mach2dat: Association with MACH output
- Mach DAC
- Main Page
- Make file tutorial
- Makefile.tool
- Mantra.cpp
- MappabilityScores
- Mapping Quality Scores
- Mary Kate Wing
- Merlin
- MetaMinimac
- Meta Analysis of SNPxEnvironment Interaction
- Minimac
- Minimac2
- Minimac3
- Minimac3 - Full List of Options
- Minimac3 ChangeLog
- Minimac3 Cookbook : Chromosome X Imputation
- Minimac3 Cookbook : Converting Files to VCF
- Minimac3 Cookbook : Pre-Phasing
- Minimac3 Examples
- Minimac3 Imputation Cookbook
- Minimac3 Info (Older Version)
- Minimac3 Info File
- Minimac3 Usage
- Minimac4
- Minimac4 - Full List of Options
- Minimac4 Documentation
- Minimac: 1000 Genomes Imputation Cookbook
- Minimac: Tutorial
- Minimac Command Reference
- Minimac Diagnostics
- Mount S3 Volume
- MutationFilter
- NHLBI Exome Sequencing Project
- NHLBI Informatics Resource
- New Fugue
- Outcomes For Mapping A Paired End
- Parameters.h
- PedScript
- PhoneHome
- Phred scale
- Pileup
- PileupBasedVariantCalling
- Polymutt
- Polymutt2
- Polymutt beta
- Power Calculations: Quantitative Traits
- QPLOT
- RAREFY
- RAREFY COMMAND
- RAREFY DOCUMENTATION
- RAREFY DOWNLOAD
- RAREFY FAQ
- RAREFY TUTORIAL