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- SeqShop: Analysis of Structural Variation Practical, June 2014 (61 revisions)
- SardiNIA (60 revisions)
- METAL Documentation (59 revisions)
- LASER (57 revisions)
- RAREMETAL (57 revisions)
- SeqShop: Calling Your Own Genome, May 2015 (56 revisions)
- FastQValidator (56 revisions)
- RareMETALS2 (55 revisions)
- GotCloud: Genetic Reference and Resource Files (55 revisions)
- Arf (53 revisions)
- LibStatGen: FASTQ (52 revisions)
- Creating an AMI on EC2 (51 revisions)
- FTEC (50 revisions)
- SeqShop: May 2015 (50 revisions)
- C++ Library: libStatGen (50 revisions)
- MaCH FAQ (49 revisions)
- GotCloud: Alignment Pipeline (49 revisions)
- Minimac2 (47 revisions)
- Shuang Feng (47 revisions)
- RAREMETAL Command Reference (46 revisions)
- Sequencing Workshop Analysis of Indels (46 revisions)
- LibStatGen Download (44 revisions)
- Test EPACTS for DIAGRAM (43 revisions)
- Thunder (43 revisions)
- RAREMETAL Change Log (43 revisions)
- Karma-colorspace (43 revisions)
- StarCluster (42 revisions)
- BamGenotypeCheck (42 revisions)
- Minimac3 Usage (42 revisions)
- Minimac4 (41 revisions)
- Amazon Snapshot (40 revisions)
- SeqShop: Ancestry On Your Own Genome, December 2014 (40 revisions)
- C++ Class: SamFile (40 revisions)
- METAL Quick Start (39 revisions)
- UMAKE (39 revisions)
- GotCloud: Alignment Sub-Pipelines (38 revisions)
- Sequence Analysis Practice 2011/03/09 (38 revisions)
- Karma (37 revisions)
- SeqShop: Analysis of Structural Variation Practical, December 2014 (37 revisions)
- SeqShop: Sequence Mapping and Assembly Practical, December 2014 (36 revisions)
- SeqShop: Variant Calling and Filtering for INDELs Practical, June 2014 (35 revisions)
- Vmatch (35 revisions)
- RAREMETALWORKER command reference (34 revisions)
- SeqShop: Estimates of Genetic Ancestry Practical, December 2014 (34 revisions)
- SeqShop: December 2014 (34 revisions)
- BamUtil: dedup (34 revisions)
- Analyses of Indels (34 revisions)
- Make file tutorial (33 revisions)
- SEQMIX (33 revisions)
- Minimac3 Info File (33 revisions)
- Biostatistics 866: Main Page (33 revisions)
- SeqShop: Variant Calling and Filtering for SNPs Practical, December 2014 (33 revisions)
- RAREMETALWORKER SPECIAL TOPICS (33 revisions)
- Minimac3 Imputation Cookbook (33 revisions)
- SAM Validation Criteria (33 revisions)
- Releasing GotCloud (32 revisions)
- GTDT (32 revisions)
- RAREMETAL FAQ (31 revisions)
- Abecasis Group Awards (31 revisions)
- SeqShop: Variant Calling and Filtering for INDELs Practical, December 2014 (31 revisions)
- Biostatistics 830 - Code Snippets (30 revisions)
- RAREFY COMMAND (30 revisions)
- Polymutt2 (30 revisions)
- BamUtil: recab (30 revisions)
- IMPUTE2: 1000 Genomes Imputation Cookbook (29 revisions)
- CSG Tech Talks (29 revisions)
- C++ Class: CigarRoller (29 revisions)
- RAREFY DOCUMENTATION (29 revisions)
- ExomePicks (28 revisions)
- BamUtil: validate (28 revisions)
- Raremetal Incoming updates (28 revisions)
- BamUtil: convert (27 revisions)
- BAM Review Action Items (27 revisions)
- Minimac3 ChangeLog (27 revisions)
- SAM (27 revisions)
- BamUtil: stats (26 revisions)
- GotCloud: Amazon Demo (26 revisions)
- SeqShop: Genetic Association Analysis Practical, June 2014 (26 revisions)
- BamUtil: bam2FastQ (26 revisions)
- Using Git Example (25 revisions)
- BamUtil: clipOverlap (25 revisions)
- SeqShop: June 2014 (25 revisions)
- M3vcftools Usage (25 revisions)
- GotCloud: Versions (24 revisions)
- EMMAX (23 revisions)
- MutationFilter (23 revisions)
- SeqShop: Genetic Association Analysis Practical, December 2014 (22 revisions)
- BamUtil: trimBam (22 revisions)
- Bar Harbor Statistical Genetics Workshop (22 revisions)
- Generic Exome Analysis Plan (22 revisions)
- Minimac: Tutorial (22 revisions)
- Introduction to new students (21 revisions)
- C++ Class: SamFileHeader (20 revisions)
- C++ Library: general Change Log (20 revisions)
- Tutorial: GotCloud UW CMG (20 revisions)
- SeqShop: Ancestry On Your Own Genome, June 2014 (20 revisions)
- C++ Class: SamRecord (20 revisions)
- Creating a Snapshot on EC2 (20 revisions)
- Amazon Storage (20 revisions)
- SeqShop: Analysis of Structural Variation Practical, May 2015 (20 revisions)
- VcfCooker (19 revisions)
- Tutorial: EMMAX GotCloud STOM (19 revisions)
- RvTests (19 revisions)
- SeqShop: Aligning Your Own Genome, December 2014 (19 revisions)
- Tandem Repeat Concepts (19 revisions)
- VICES (19 revisions)
- GotCloud: Source Releases (19 revisions)
- Tutorial: Low Pass Sequence Analysis Answers (19 revisions)
- GlfSingle (19 revisions)
- Bam read count (18 revisions)
- SeqShop: Ancestry On Your Own Genome, May 2015 (18 revisions)
- GotCloud: FAQs (18 revisions)
- GotCloud: Variant Calling Options (17 revisions)
- Minimac Command Reference (17 revisions)
- BamUtil: filter (17 revisions)
- C++ Class: InputFile (17 revisions)
- SeqShop: Sequence Mapping and Assembly Practical, May 2015 (17 revisions)
- LibStatGen Repository (17 revisions)
- GlfTrio (17 revisions)
- Evaluating a Read Mapper on Simulated Data (17 revisions)
- Minimac3 Info (Older Version) (17 revisions)
- FamLDCaller (17 revisions)
- RAREFY (17 revisions)
- LibStatGen: general (17 revisions)
- MEAGA (17 revisions)
- ChunkChromosome (16 revisions)
- SeqShop: Aligning Your Own Genome, June 2014 (16 revisions)
- LibStatGen: ASP (16 revisions)
- VcfRefGen (16 revisions)
- BamUtil: mergeBam (15 revisions)
- GlfMultiples (15 revisions)
- SeqShop: Calling Your Own Genome, June 2014 (15 revisions)
- METAL (15 revisions)
- Short Workshops (15 revisions)
- LibStatGen: VCF (15 revisions)
- C++ Library: FASTQ Change Log (15 revisions)
- SardiNIA project meeting July 15-16, 2013 (14 revisions)
- How To Use Git (14 revisions)
- M3vcftools (13 revisions)
- Mach DAC (13 revisions)
- Genezoom (13 revisions)
- SeqShop: Variant Calling and Filtering for SNPs Practical, May 2015 (13 revisions)
- GotCloud: GenomeSTRiP Pipeline (13 revisions)
- Git FAQs (13 revisions)
- METAL Command Reference (13 revisions)
- MaCH: machX (13 revisions)
- CalcMatch (13 revisions)
- Minimac3 Cookbook : Chromosome X Imputation (13 revisions)
- GotCloud: Creating a New Pipeline (12 revisions)
- Minimac3 Examples (12 revisions)
- RAREFY DOWNLOAD (12 revisions)
- RelativeFinder (12 revisions)
- MaCH: Input Files (12 revisions)
- SAM/BAM Classes FAQs (12 revisions)
- LiftOver (12 revisions)
- Base Caller Summaries (12 revisions)
- BamUtil: writeRegion (12 revisions)
- GLF (12 revisions)
- Sean Caron (11 revisions)
- Class Notes (11 revisions)
- Tutorial: EMMAX GotCloud STOM: Lecture 8 (11 revisions)
- Verifying Sample Identities - Implementation (11 revisions)
- SAV File Format (11 revisions)
- BamUtil: diff (11 revisions)
- MaCH: 1000 Genomes Imputation Cookbook (11 revisions)
- SeqShop: Variant Calling and Filtering for INDELs Practical, May 2015 (11 revisions)
- LibStatGen Troubleshooting (11 revisions)
- RAREFY TUTORIAL (11 revisions)
- UMAKE-glfSingle (10 revisions)
- Trial Enrichment (10 revisions)
- LibStatGen: GLF (10 revisions)
- Amazon Single Node (10 revisions)
- 1000 Genomes Project Pilot 1 SNP Calling (10 revisions)
- Minimac4 - Full List of Options (10 revisions)
- C++ Class: FastQFile (10 revisions)
- Haploxt (10 revisions)
- Sam Library Usage Examples (10 revisions)
- BamUtil: polishBam (10 revisions)
- Biostatistics 666: Linkage Disequilibrium (10 revisions)
- BAFRegress (9 revisions)
- GotCloud: Amazon (9 revisions)
- Dajiang Liu (9 revisions)
- Goncalo Abecasis (9 revisions)
- Regions of high linkage disequilibrium (LD) (9 revisions)
- ContaminationDetection (9 revisions)
- Using Gotcloud on Flux (9 revisions)
- New Fugue (9 revisions)
- BamUtil: splitBam (9 revisions)
- FamRvTest command (9 revisions)
- Summary Statistics Files Specification for RAREMETAL and rvtests (9 revisions)
- Rare variant tests (9 revisions)
- Idriver (8 revisions)
- Examples of Read Mapping with Karma and BWA (8 revisions)
- BaseQualityCheck (8 revisions)
- Minimac3 Cookbook : Converting Files to VCF (8 revisions)
- Debuggers (8 revisions)
- Bayesdenovo (8 revisions)
- Biostatistics 666: Introductory Lecture (8 revisions)
- Biostatistics 501: Main Page (8 revisions)
- METAL FAQ (8 revisions)
- Gzip (8 revisions)
- Biostatistics 666: Modeling Recombination and Migration in the Coalescent (8 revisions)
- Sayantan Das (8 revisions)
- GotCloud: Configuration (7 revisions)
- SeqShop: Aligning Your Own Genome, May 2015 (7 revisions)
- RAREMETALWORKER X (7 revisions)
- Jennifer Bragg-Gresham (7 revisions)
- Mount S3 Volume (7 revisions)
- SplitPed (7 revisions)
- SeqShop: Association Analysis, May 2015 (7 revisions)
- BamUtil: dumpAsp (7 revisions)
- SAM/BAM Convert Sequence (7 revisions)
- Minimac4 Documentation (7 revisions)
- SeqShop: Friday - Practicing what we learned, June 2014 (7 revisions)
- PileupBasedVariantCalling (7 revisions)
- Biostatistics 666: Hardy-Weinberg Equilibrium (7 revisions)
- Better X Sessions from Home (NX) (7 revisions)
- FastQ Validation Criteria (6 revisions)
- Genotype Likelihood Based Allele Balance (6 revisions)
- Biostatistics 666: Advanced Coalescent, Changing Population Size (6 revisions)
- BAM (6 revisions)
- Git Cheat Sheet (6 revisions)
- Biostatistics 666: Maximum Likelihood Allele Frequency Estimation (6 revisions)
- Minimac3 - Full List of Options (6 revisions)
- GotCloud: RedHat Package (6 revisions)
- GotCloud: Filters (6 revisions)
- Scott Vrieze (6 revisions)
- BamUtil: squeeze (6 revisions)
- SeqShop: Estimates of Genetic Ancestry Practical, May 2015 (6 revisions)
- Tutorial: EMMAX GotCloud STOM: Lecture 5 (6 revisions)
- Garlic (6 revisions)
- SNP Call Set Properties (6 revisions)
- Minimac3 Cookbook : Pre-Phasing (6 revisions)
- Genotype Likelihood based Allele Frequency (6 revisions)
- An example of using libcsg (6 revisions)
- Code Sample: Generating QQ Plots in R (6 revisions)
- BamUtil: indelDiscordance (6 revisions)
- Understanding vcf-summary output (6 revisions)
- Computer How-Tos (6 revisions)
- PedScript (5 revisions)
- BamUtil: gapInfo (5 revisions)
- Installing MinGW & MSYS on Windows (5 revisions)
- Configure GotCloud (5 revisions)
- NHLBI Informatics Resource (5 revisions)
- Understanding VerifyBamID output (5 revisions)
- Fst (5 revisions)
- Biostatistics 666: Introduction to De Novo Assembly (5 revisions)
- Meta Analysis of SNPxEnvironment Interaction (5 revisions)
- BamUtil: asp (5 revisions)
- BamPileup (5 revisions)
- Biostatistics 666: Modeling Variation in the Coalescent (5 revisions)
- M3VCF Files (5 revisions)
- StatgenTools (5 revisions)
- Vpeep (5 revisions)
- BamUtil: FAQ (5 revisions)
- Read Mapping (5 revisions)
- Biostatistics 666: Haplotype Association Tests (5 revisions)
- Mapping Quality Scores (5 revisions)
- Rvtests (5 revisions)
- Mach2dat: Association with MACH output (5 revisions)
- Samtools-hybrid (4 revisions)
- Basic Linux Intro (4 revisions)
- Ben Lerch (4 revisions)
- AWS Resources (4 revisions)
- Biostatistics 666: Introduction to the E-M Algorithm (4 revisions)
- BamUtil: dumpHeader (4 revisions)
- RAREFY FAQ (4 revisions)
- Biostatistics 666: Haplotype Estimation (4 revisions)
- SAV Command Line Interface (4 revisions)
- Genotype Likelihood based Inbreeding Coefficient (4 revisions)
- Tutorial: EMMAX GotCloud STOM: Lecture 6 (4 revisions)
- Variant Call Pipeline (4 revisions)
- 830 - Haplotyper::SampleHaplotypes() (4 revisions)
- BamUtil: revert (4 revisions)
- StatsTools (4 revisions)
- 830 - Haplotyper::ScoreLeftConditional() (4 revisions)
- Links to Sequence Analysis Tools (4 revisions)
- Biostatistics 666: Introduction to the Coalescent (4 revisions)
- 830 - MINIMAC::main() (4 revisions)
- TabAnno (4 revisions)
- CheckVCF.py (4 revisions)
- Biostatistics 666: Whole Genome Sequencing (4 revisions)
- Biostatistics 666: Advanced Coalescent, Computation with the Coalescent (4 revisions)
- C++ Class: Pedigree Example (4 revisions)
- Alan Kwong (4 revisions)
- Power Calculations: Quantitative Traits (4 revisions)
- 830 - Haplotyper::SampleOneHaplotype() (4 revisions)
- Tramp (4 revisions)
- VerifyIDintensity (4 revisions)
- CigarRoller Proposed Update (4 revisions)
- Biostatistics 666: Linkage Tests for Pairs of Individuals (4 revisions)
- BamUtil: splitChromosome (4 revisions)
- Pileup (4 revisions)
- TrioCaller:Archive (4 revisions)
- Biostatistics 666: Linkage Analysis in Sibling Pairs (4 revisions)
- Minimac Diagnostics (4 revisions)
- Savvy C++ Library (4 revisions)
- Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium (4 revisions)
- BamUtil: dumpRefInfo (3 revisions)
- Understanding QPLOT output (3 revisions)
- 830 - Haplotyper::ImputeGenotypes() (3 revisions)
- Zlib (3 revisions)
- 830 - Haplotyper::SummarizeOptions() (3 revisions)
- GBR60vc.conf (3 revisions)
- 830 - Haplotyper::RandomSetup() (3 revisions)
- BamUtil: findCigars (3 revisions)
- CHARGE (3 revisions)
- Lars Fritsche (3 revisions)
- Screen Commands (3 revisions)
- TOPMed Site Visit 2018 (3 revisions)
- Ligate Minimac (3 revisions)
- BAM to FASTQ (3 revisions)
- Xiaowei Zhan (3 revisions)
- Rare Variant Analysis and Meta-Analysis (3 revisions)
- MappabilityScores (3 revisions)
- METAL CUSTOMVARIABLE (3 revisions)
- Biostatistics 666: Association Tests in Structured Populations (3 revisions)
- Biostatistics 666: Power of Genomewide Association Studies (3 revisions)
- Code Sample: Generating Manhattan Plots in R (3 revisions)
- FASTA (3 revisions)
- Ann Arbor Travel Basics (3 revisions)
- 830 - Haplotyper::ImputeGenotypes() (internal) (3 revisions)
- Biostatistics 666: Variance Component Analyses (3 revisions)
- TinySimulator (3 revisions)
- GWAS (3 revisions)
- Kyoto Encyclopedia of Genes and Genomes (3 revisions)
- Sara Rashkin (3 revisions)
- Biostatistics 666: Applications of the Lander-Green Algorithm (3 revisions)
- BamUtil: dumpIndex (3 revisions)
- 830 - Haplotyper::SetupPrior() (2 revisions)
- 830 - Haplotyper::SampleChromosomes() (2 revisions)
- 830 - MarkovModel::Condition() (2 revisions)
- Biostatistics 666: Analysis of Copy Number Using Sequence Data (2 revisions)
- Example (2 revisions)
- 830 - MaqIndex::CompareToIndex() (2 revisions)
- Mary Kate Wing (2 revisions)
- MaCH Options (2 revisions)
- NHLBI Exome Sequencing Project (2 revisions)
- GotCloud: Reference Files (2 revisions)
- Tom Blackwell (2 revisions)
- Makefile.tool (2 revisions)
- Goncalo Abecasis: Interview with Christiana Fogg (2 revisions)
- Mantra.cpp (2 revisions)
- SAM: Filtering Reads (2 revisions)
- StringMap.h (2 revisions)
- Biostatistics 666: Rare Variant Burden Tests (2 revisions)
- MaCH: Pedigree with Integer Allele Codes (2 revisions)
- Gene Ontology (2 revisions)
- 830 - MarkovModel::Transpose() (2 revisions)
- 830 - Haplotyper::ScoreLeftConditional() (smart, complicated) (2 revisions)
- LiftRsNumber.py (2 revisions)
- RareSimu (2 revisions)
- Editing Sequence Analysis Practice 2011/03/10 (2 revisions)
- GlfMerge (2 revisions)
- LiftMap.py (2 revisions)
- 830 - MarkovModel::WalkLeft() (2 revisions)
- Biostatistics 666: Contemporary Human Genetics (2 revisions)
- 830 - BestAlignment::MaqAlignment() (2 revisions)
- METAL GENOMICCONTROL (2 revisions)
- Polymutt beta (2 revisions)
- Biostatistics 666: Core Competencies (2 revisions)
- 830 - BestAlignment::ClearPositions() (2 revisions)
- Biostatistics 815 Term Project (2 revisions)
- Parameters.h (2 revisions)
- IMPUTE2 (2 revisions)
- 830 - BestAlignment::EvaluateAlignment() (detailed comparison) (2 revisions)
- 830 - Haplotyper::ConditionOnData() (2 revisions)
- 830 - MaqIndex::LookupWord() (2 revisions)
- Stouffer Method for Meta-Analysis (2 revisions)
- Gzip File (2 revisions)
- VCF (2 revisions)
- Biostatistics 666: Advanced Haplotype Estimation (2 revisions)
- 830 - Haplotyper::ImputeGenotypes() (edge) (2 revisions)
- VcfGenomeStat (2 revisions)
- BamUtil: readIndexedBam (2 revisions)
- BamUtil: readReference (2 revisions)
- Merlin (2 revisions)
- METAL ADDFILTER (2 revisions)
- Biostatistics 666: Genotype Imputation (2 revisions)
- Genotype Likelihood based Hardy-Weinberg Test (2 revisions)
- SplitRef (2 revisions)
- Biostatistics 666: Multipoint Analysis in Sibling Pairs (2 revisions)
- Biostatistics 666: Relationship Checking (2 revisions)
- Biostatistics 615/815 Winter 2011 (1 revision)
- HAPMIX (1 revision)
- Imputation Server: Example (1 revision)
- Rare-metal-worker (1 revision)
- Biostatistics 830: Fall 2013 Edition (1 revision)
- Utility Library (1 revision)
- 830 - BasicMapper::main() (1 revision)
- IGFPipe (1 revision)
- Phred scale (1 revision)
- RareMetals (1 revision)
- METAL COLUMNCOUNTING (1 revision)
- 830 - BestAlignment::EvaluateAlignment() (main loop) (1 revision)
- How to use aspera (1 revision)
- MERLIN format (1 revision)
- METAL EFFECTLABEL (1 revision)
- Indel (1 revision)
- METAL SOURCE (1 revision)
- Outcomes For Mapping A Paired End (1 revision)
- SavR (1 revision)
- Biostatistics 666: Copy Number Variation (1 revision)
- 830 - MarkovModel::CountRecombinants() (1 revision)
- 830 - MarkovModel::WalkRight() (1 revision)
- METAL Glucose Example Script (1 revision)
- C++ Class Averages (1 revision)
- METAL LOGPVALUE (1 revision)
- Biostatistics 666: The Lander-Green Algorithm (1 revision)
- 830 - MaqIndex::GetWord() (1 revision)
- Hardy Weinberg equilibrium (1 revision)
- PhoneHome (1 revision)
- Biostatistics 666: Likelihood Calculations for Large Pedigrees (1 revision)
- ThunderVCF (1 revision)
- 830 - MarkovModel::CountErrorsAndRecombinants() (1 revision)
- AWS Credentials (1 revision)
- Biostatistics 666: The Possible Triangle Constraint (1 revision)
- 830 - MarkovModel::CountErrors() (1 revision)
- 830 - MaqIndex::BuildIndex() (1 revision)
- Biostatistics 830: Core Competencies (1 revision)
- 830 - BestAlignment::isNewPosition() (1 revision)
- BamUtil: explainFlags (1 revision)
- Biostatistics 866: Core Competencies (1 revision)
- Dosage convertor (1 revision)
- GotCloud: AMIs (1 revision)
- 830 - Haplotyper::Transpose() (1 revision)
- Vcf2geno (1 revision)
- FamRvTest tutorial (1 revision)
- Tutorial: EMMAX GotCloud STOM: Lecture 2 (1 revision)
- 830 - BestAlignment::IterateCache() (1 revision)
- METAL VERBOSE (1 revision)
- MetaMinimac (1 revision)
- 830 - MarkovModel::Impute() (1 revision)
- Ancestry (1 revision)
- Biostatistics 666: Analysis of Low Pass Sequence Data (1 revision)
