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From Genome Analysis Wiki
Jump to navigationJump to search- 16:18, 23 March 2010 diff hist +133 N Merlin Created page with 'A program for linkage and association analysis in human pedigrees. See [http://www.sph.umich.edu/csg/abecasis/Merlin/ Merlin Website]'
- 16:17, 23 March 2010 diff hist +449 N Phred scale Created page with 'A scale commonly used to measure data quality and error rates in sequence analysis. It was popularized by Phil Green's PHRED base-calling software. It is defined as: <math> …' current
- 12:42, 23 March 2010 diff hist 0 MediaWiki:Sidebar
- 12:42, 23 March 2010 diff hist +11 MediaWiki:Sidebar
- 12:42, 23 March 2010 diff hist +2 MediaWiki:Sidebar
- 12:41, 23 March 2010 diff hist +30 MediaWiki:Sidebar
- 12:38, 23 March 2010 diff hist +17 Abecasis Lab →Staff
- 10:28, 23 March 2010 diff hist +122 Abecasis Lab →Former Research Fellows
- 10:25, 23 March 2010 diff hist +450 Abecasis Lab →Former Research Fellows
- 10:16, 23 March 2010 diff hist +698 Abecasis Lab →Former Doctoral Students
- 10:09, 23 March 2010 diff hist +188 Abecasis Lab →Former Doctoral Students
- 10:08, 23 March 2010 diff hist +27 Abecasis Lab →Former Doctoral Students
- 07:43, 23 March 2010 diff hist +382 N Biostatistics 666: The Possible Triangle Constraint Created page with '== Content == Show how simple genetic models can be used to predict similarity between relative pairs and IBD sharing among sibling pairs. Introduce the possible triangle constr…' current
- 07:15, 23 March 2010 diff hist +1 Biostatistics 666: Linkage Tests for Pairs of Individuals →Recommended Reading
- 07:15, 23 March 2010 diff hist -132 Biostatistics 666: Linkage Tests for Pairs of Individuals →Recommended Reading
- 07:15, 23 March 2010 diff hist +648 N Biostatistics 666: Linkage Tests for Pairs of Individuals Created page with '== Overview == This lecture introduces simple linkage tests in the context of affected sibling pairs. One test, originally described by Bishop and Williamson (1990) focuses on i…'
- 07:11, 23 March 2010 diff hist +172 Biostatistics 666: Main Page →Class Notes
- 07:09, 23 March 2010 diff hist +64 N File:666.16.pdf Introduces multipoint analysis, in the context of sibling pairs.
- 07:09, 23 March 2010 diff hist +135 N File:666.15.pdf Shows how a simple disease model can be used to predict IBD probabilities for relative pairs. Introduces possible triangle constraint. current
- 07:17, 18 March 2010 diff hist +31 N MapabilityScores moved MapabilityScores to MappabilityScores current
- 07:17, 18 March 2010 diff hist 0 m MappabilityScores moved MapabilityScores to MappabilityScores current
- 07:17, 18 March 2010 diff hist 0 N File:666.14.pdf current
- 07:17, 18 March 2010 diff hist +90 Biostatistics 666: Main Page →Class Notes
- 04:37, 11 March 2010 diff hist -7 LocusZoom →Generate single plots using our publicly-available lipids GWAS data
- 04:35, 11 March 2010 diff hist -66 LocusZoom
- 04:28, 11 March 2010 diff hist -13 LocusZoom →Upload your own meta-analysis file and generate single plots using a web-based form
- 05:39, 8 March 2010 diff hist 0 ExomePicks →Download
- 04:09, 4 March 2010 diff hist +96 ExomePicks
- 04:07, 4 March 2010 diff hist 0 ExomePicks →Download
- 09:45, 3 March 2010 diff hist -1 ExomePicks →Download
- 09:45, 3 March 2010 diff hist +1 ExomePicks →Download
- 09:44, 3 March 2010 diff hist +9 ExomePicks →Download
- 09:44, 3 March 2010 diff hist +3,009 ExomePicks
- 09:28, 3 March 2010 diff hist +11 ExomePicks →Input Files
- 09:28, 3 March 2010 diff hist +2,420 N ExomePicks Created page with ''''ExomePicks''' is a program that suggests individuals to be sequenced in a large pedigree. '''ExomePicks''' assumes that a genotyping chip or another cost effective means will …'
- 03:00, 22 February 2010 diff hist +913 N Biostatistics 666: Association Tests in Structured Populations Created page with ' == Overview == This lecture introduces the problem of population stratification in the context of genetic association studies. It also discusses three possible strategies for h…'
- 02:56, 22 February 2010 diff hist +234 N File:666.13.pdf Introduces the problem of population stratification in the context of an association study. Discusses three possible solutions: a) Family based association tests. b) The genomic control method. c) Genotype based matching approaches.
- 02:54, 22 February 2010 diff hist +95 Biostatistics 666: Main Page →Class Notes
- 16:52, 19 February 2010 diff hist +1,228 N Outcomes For Mapping A Paired End Created page with '== Basics == Paired end reads have an expected relative orientation (for example, FR are expected to map to opposite strands of the genome) and distance (for example, 500 bp +/-…' current
- 08:20, 18 February 2010 diff hist +12 Biostatistics 666: Main Page →Course History
- 08:19, 18 February 2010 diff hist +940 N Biostatistics 666: Haplotype Association Tests Created page with '== Objective == This page introduces the idea of haplotype association tests. It includes a discussion of when haplotype association tests might be preferable to single marker a…'
- 08:15, 18 February 2010 diff hist +39 N File:666.12.pdf Introduces Haplotype Association Tests.
- 08:15, 18 February 2010 diff hist +79 Biostatistics 666: Main Page →Class Notes
- 02:42, 17 February 2010 diff hist -738 1000 Genomes Project Pilot 1 SNP Calling
- 02:40, 17 February 2010 diff hist -191 1000 Genomes Project Pilot 1 SNP Calling
- 17:45, 16 February 2010 diff hist -3 1000 Genomes Project Pilot 1 SNP Calling
- 23:01, 15 February 2010 diff hist -1 Biostatistics 666: Advanced Coalescent, Computation with the Coalescent →Guest Lecturer current
- 23:00, 15 February 2010 diff hist -1 Biostatistics 666: Advanced Coalescent, Changing Population Size →Guest Lecturer current
- 22:59, 15 February 2010 diff hist 0 File:666.10.pdf uploaded a new version of "File:666.10.pdf": Introduction to E-M Algorithm in Genetics. This version fixes reference to Excoffier and Slatkin paper.
- 22:58, 15 February 2010 diff hist 0 File:666.09.pdf uploaded a new version of "File:666.09.pdf": Fixed reference to Excoffier paper.
- 22:53, 15 February 2010 diff hist +42 N File:666.11.pdf Haplotyping Algorithms. February 16, 2010
- 22:48, 15 February 2010 diff hist +754 N Biostatistics 666: Haplotype Estimation Created page with '== Objective == This lecture introduces several strategies for estimating individual haplotypes and their frequencies. At heart, all population-based haplotyping algorithms look…'
- 22:42, 15 February 2010 diff hist +221 Biostatistics 666: Introduction to the E-M Algorithm
- 22:40, 15 February 2010 diff hist +72 Biostatistics 666: Main Page →Class Notes
- 09:46, 11 February 2010 diff hist 0 N File:666.10.pdf
- 06:15, 11 February 2010 diff hist +283 N Biostatistics 666: Introduction to the E-M Algorithm Created page with '== Objective == Introduce the E-M algorithm in genetics == Slides == Slide in PDF Format == Recommended Reading == Slatkin M, Excoffier L (1996) �Test…'
- 01:26, 11 February 2010 diff hist +4 Biostatistics 666: Advanced Coalescent, Changing Population Size
- 01:26, 11 February 2010 diff hist -387 Biostatistics 666: Advanced Coalescent, Computation with the Coalescent →Recommended Reading
- 01:25, 11 February 2010 diff hist +317 Biostatistics 666: Advanced Coalescent, Computation with the Coalescent
- 01:24, 11 February 2010 diff hist +642 N Biostatistics 666: Advanced Coalescent, Computation with the Coalescent Created page with '== Objective == == Slides == Slides in PDF format == Recommended Reading == Richard R. Hudson (1990) Gene genealogies and the coalescent process ''in'' O…'
- 01:23, 11 February 2010 diff hist -4 Biostatistics 666: Advanced Coalescent, Changing Population Size →Objectives
- 01:22, 11 February 2010 diff hist +6 Biostatistics 666: Advanced Coalescent, Changing Population Size →Notes
- 01:22, 11 February 2010 diff hist -1 Biostatistics 666: Advanced Coalescent, Changing Population Size →Guest Lecturer =
- 01:21, 11 February 2010 diff hist +334 N Biostatistics 666: Advanced Coalescent, Changing Population Size Created page with '== Guest Lecturer === This will be a guest lecture by Sebastian Zoellner, who is our department's resident expert on the coalescent.s == Objectives == Provide an introduction …'
- 01:19, 11 February 2010 diff hist +286 Biostatistics 666: Main Page →Class Notes
- 01:17, 11 February 2010 diff hist +123 N File:666.08.pdf Advanced guest lecture by Sebastian Zoellner. Focused on computation methods related to the coalescent. February 4, 2010. current
- 01:16, 11 February 2010 diff hist +156 N File:666.07.pdf Advanced lecture on the coalescent by guest lecturer, Sebastian Zoellner. Focused on coalescent modeling with changing population sizes. February 2, 2009. current
- 12:01, 9 February 2010 diff hist 0 File:666.09.pdf uploaded a new version of "File:666.09.pdf": Fixed minor typos. February 9, 2010
- 04:59, 9 February 2010 diff hist +6 Biostatistics 666: Modeling Variation in the Coalescent →Slides
- 04:58, 9 February 2010 diff hist 0 Biostatistics 666: Modeling Variation in the Coalescent →Slides
- 04:58, 9 February 2010 diff hist +6 Biostatistics 666: Modeling Recombination and Migration in the Coalescent →Slides
- 04:57, 9 February 2010 diff hist +6 Biostatistics 666: Maximum Likelihood Allele Frequency Estimation →Slides
- 04:57, 9 February 2010 diff hist 0 Biostatistics 666: Maximum Likelihood Allele Frequency Estimation →Slides
- 04:57, 9 February 2010 diff hist +712 N Biostatistics 666: Maximum Likelihood Allele Frequency Estimation Created page with '== Objective == This lecture examines maximum likelihood based estimation of allele frequencies in several simple settings, such as estimation of allele frequencies from samples…'
- 04:49, 9 February 2010 diff hist +189 N File:666.09.pdf This lecture reviews maximum likelihood estimation and applies maximum likelihood concepts to derive estimates of allele frequency in several simple settings. Last update February 9, 2010.
- 04:48, 9 February 2010 diff hist +1 Biostatistics 666: Main Page →Class Notes
- 04:48, 9 February 2010 diff hist +97 Biostatistics 666: Main Page →Class Notes
- 15:53, 2 February 2010 diff hist -60 MediaWiki:Sidebar
- 15:52, 2 February 2010 diff hist +31 MediaWiki:Sidebar
- 15:51, 2 February 2010 diff hist 0 MediaWiki:Sidebar
- 15:50, 2 February 2010 diff hist +242 N MediaWiki:Sidebar Created page with '* navigation ** mainpage|mainpage-description ** portal-url|portal ** currentevents-url|currentevents ** recentchanges-url|recentchanges ** randompage-url|randompage ** helppage|…'
- 15:28, 2 February 2010 diff hist +31 Evaluating a Read Mapper on Simulated Data
- 15:17, 2 February 2010 diff hist +128 Evaluating a Read Mapper on Simulated Data →Grouping
- 15:05, 2 February 2010 diff hist +1,393 N Evaluating a Read Mapper on Simulated Data Created page with '== Grouping == When evaluating read mappers, we should always focus on well defined sets of reads: * Reads with no polymorphisms. * Reads with 1, 2, 3 or more SNPs. * Reads wit…'
- 13:06, 28 January 2010 diff hist 0 Links to Sequence Analysis Tools →Base Calling Tools
- 13:06, 28 January 2010 diff hist +796 Links to Sequence Analysis Tools
- 04:23, 28 January 2010 diff hist +60 N File:666.06.pdf Coalescent with Recombination or Migration January 26, 2010
- 03:05, 28 January 2010 diff hist -1 Biostatistics 666: Modeling Recombination and Migration in the Coalescent →Recommended Reading
- 02:46, 28 January 2010 diff hist +11 Biostatistics 666: Modeling Recombination and Migration in the Coalescent →Objective
- 02:45, 28 January 2010 diff hist +227 Biostatistics 666: Modeling Recombination and Migration in the Coalescent
- 02:44, 28 January 2010 diff hist +1 Biostatistics 666: Modeling Recombination and Migration in the Coalescent →Recommended Reading
- 02:43, 28 January 2010 diff hist +543 Biostatistics 666: Modeling Recombination and Migration in the Coalescent →Recommended Reading
- 02:37, 28 January 2010 diff hist +56 N Biostatistics 666: Modeling Recombination and Migration in the Coalescent Created page with '== Objective == == Slides == == Recommended Reading =='
- 02:36, 28 January 2010 diff hist +106 Biostatistics 666: Main Page →Class Notes
- 02:21, 26 January 2010 diff hist +215 Biostatistics 666: Modeling Variation in the Coalescent →Recommended Reading
- 02:20, 26 January 2010 diff hist +407 N Biostatistics 666: Modeling Variation in the Coalescent Created page with '== Objective == This class builds on previous descriptions of the coalescent. In the class we model the impact of mutations on the coalescent and use it to study: * What is the…'
- 02:15, 26 January 2010 diff hist +214 N File:666.05.pdf This lecture covers three concepts: * Estimating theta using sequence data as input. * Modeling frequency spectra using simulations * Analytically modeling the distribution of total variant count January 26, 2010
- 02:12, 26 January 2010 diff hist +88 Biostatistics 666: Main Page →Class Notes
- 11:36, 21 January 2010 diff hist +141 N Links to Sequence Analysis Tools Created page with ' http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration Quality Score Calibration Tool at the Broad Institute.'
- 11:35, 21 January 2010 diff hist +65 Main Page →Sequence Analysis Tools
- 11:31, 21 January 2010 diff hist +108 Main Page →Miscellaneous Utilities
- 11:29, 21 January 2010 diff hist +2 Read Mapping
- 11:28, 21 January 2010 diff hist +505 N Read Mapping Created page with '== Read mappers that we like are == [http://bio-bwa.sourceforge.net BWA] - A much faster aligner developed by Richard Durbin and Heng Li. Karma - Currently under development…'
- 11:23, 21 January 2010 diff hist +4 Main Page →Read Mapping
- 09:37, 21 January 2010 diff hist +49 N File:666.04.pdf Introduction to the Coalescent. January 21, 2010
- 04:23, 19 January 2010 diff hist 0 File:666.03.pdf uploaded a new version of "File:666.03.pdf": Introduction to Linkage Disequilibrium. Further tweaks as of January 19, 2010. The lecture is presently too long and should be split into two.
- 03:13, 19 January 2010 diff hist 0 File:666.03.pdf uploaded a new version of "File:666.03.pdf": Updated Lecture Notes, as of January 19, 2010.
- 01:44, 19 January 2010 diff hist +412 N Biostatistics 666: Introduction to the Coalescent Created page with '== Objective == Introduce the coalescent as a practical means to model the properties of alleles in a population. == Slides == Slides in PDF Format == Ba…'
- 01:37, 19 January 2010 diff hist +82 Biostatistics 666: Main Page →Class Notes
- 08:44, 14 January 2010 diff hist +95 N File:666.03.pdf Introduces Measures of Linkage Disequibrium and Related Concepts Last updated January 14, 2010
- 07:56, 14 January 2010 diff hist +311 Biostatistics 666: Linkage Disequilibrium →Objective
- 07:54, 14 January 2010 diff hist +840 N Biostatistics 666: Linkage Disequilibrium Created page with '== Objective == == Slides == Slides in PDF Format == Background Reading == Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Diblin…'
- 07:37, 14 January 2010 diff hist +74 Biostatistics 666: Main Page →Class Notes
- 10:55, 13 January 2010 diff hist +493 FastQValidator
- 10:52, 13 January 2010 diff hist 0 Main Page →Miscellaneous Utilities
- 10:52, 13 January 2010 diff hist +29 N FastQ validator moved FastQ validator to FastQ Validator current
- 10:52, 13 January 2010 diff hist 0 m FastQValidator moved FastQ validator to FastQ Validator
- 10:51, 13 January 2010 diff hist 0 Main Page →Miscellaneous Utilities
- 10:50, 13 January 2010 diff hist +108 Main Page →Sequence Analysis Tools
- 10:44, 13 January 2010 diff hist +44 FastQValidator
- 02:49, 12 January 2010 diff hist +22 Biostatistics 666: Hardy-Weinberg Equilibrium →Objective
- 02:49, 12 January 2010 diff hist +451 Biostatistics 666: Hardy-Weinberg Equilibrium
- 02:45, 12 January 2010 diff hist +19 Biostatistics 666: Hardy-Weinberg Equilibrium →Slides
- 02:44, 12 January 2010 diff hist +2 Biostatistics 666: Main Page →Class Notes
- 02:44, 12 January 2010 diff hist -1 Biostatistics 666: Main Page →Class Notes
- 02:44, 12 January 2010 diff hist -2 Biostatistics 666: Main Page →Class Notes
- 02:44, 12 January 2010 diff hist +28 Biostatistics 666: Main Page →Class Notes
- 02:43, 12 January 2010 diff hist +55 N File:666.02.pdf Lecture on Hardy Weinberg Equilibrium January 12, 2009
- 11:28, 7 January 2010 diff hist +6 Biostatistics 666: Main Page →Office Hours
- 10:05, 7 January 2010 diff hist +54 Biostatistics 666: Main Page
- 00:40, 7 January 2010 diff hist +27 Biostatistics 666: Main Page →Class Notes
- 00:38, 7 January 2010 diff hist +1 Biostatistics 666: Introductory Lecture →Slides
- 00:28, 7 January 2010 diff hist +42 Biostatistics 666: Introductory Lecture →Slides
- 00:26, 7 January 2010 diff hist +56 N File:666.01.pdf Biostatistics 666 Introductory Lecture as of 2010/01/06.
- 00:25, 7 January 2010 diff hist +899 Biostatistics 666: Main Page
- 23:54, 6 January 2010 diff hist +41 Biostatistics 666: Hardy-Weinberg Equilibrium
- 23:53, 6 January 2010 diff hist +300 N Biostatistics 666: Introductory Lecture Created page with '== Objective == This lecture introduces course objectives, which are to provide students with a working understanding of the techniques commonly used by statistical geneticists.…'
- 23:50, 6 January 2010 diff hist +195 N Biostatistics 666: Hardy-Weinberg Equilibrium Created page with '== Background Reading == Please read the following paper: Wigginton JE, Cutler DJ and Abecasis GR (2005). A note on exact tests of Hardy-Weinberg equilibrium. ''Am J Hum Genet'…'
- 23:48, 6 January 2010 diff hist +51 Biostatistics 666: Main Page →Class Notes
- 23:47, 6 January 2010 diff hist +42 N 666 Redirected page to Biostatistics 666: Main Page current
- 23:45, 6 January 2010 diff hist +397 Biostatistics 666: Main Page
- 23:42, 6 January 2010 diff hist +45 Biostatistics 666: Main Page →Class Notes
- 23:41, 6 January 2010 diff hist +765 N Biostatistics 666: Main Page Created page with '== Objective == Gene mapping studies aim to study the relationship between genetic variation and susceptibility to human disease. These studies can be used to elucidate the bioc…'
- 23:39, 6 January 2010 diff hist -28 Class Notes
- 23:35, 6 January 2010 diff hist +263 Class Notes
- 23:31, 6 January 2010 diff hist +15 Class Notes →BIOSTAT 666 Statistical and Numerical Methods in Human Genetics
- 23:31, 6 January 2010 diff hist +537 N Class Notes Created page with '== BIOSTAT 666 Statistical and Numerical Methods in Human Genetics == Gene mapping studies aim to study the relationship between genetic variation and suscepti…'
- 23:30, 6 January 2010 diff hist -576 Main Page →Learn Genetics
- 23:28, 6 January 2010 diff hist +743 Main Page
- 02:52, 19 December 2009 diff hist +34 SAM
- 02:51, 19 December 2009 diff hist +76 BAM
- 02:50, 19 December 2009 diff hist +237 N SAM Created page with 'The '''SAM Format''' is a text format for storing aligned reads. The current definition of the format is at http://samtools.sourceforge.net/SAM1.pdf BAM/SAM Specification. …'
- 02:48, 19 December 2009 diff hist +670 Mapping Quality Scores
- 11:53, 18 December 2009 diff hist +147 GLF →Tools That Use GLF Files
- 19:05, 17 December 2009 diff hist -5 CHARGE →Reference current
- 19:05, 17 December 2009 diff hist +88 CHARGE
- 18:40, 17 December 2009 diff hist +44 Main Page →Read Mapping
- 18:38, 17 December 2009 diff hist +172 Mapping Quality Scores
- 18:34, 17 December 2009 diff hist +743 N Mapping Quality Scores Created page with ''''Mapping Quality Scores''' quantify the probability that a read is misplaced. They were introduced by Heng Li and Richard Durbin in their paper describing MAQ and are usually r…'
- 15:00, 15 December 2009 diff hist +262 N CHARGE Created page with ''''CHARGE''' is a consortium of several population based cohorts. The acronym stands for Cohorts for Health and Aging Related Genetic Epidemiology. == Participating Cohorts == …'
- 14:46, 15 December 2009 diff hist +46 N GWAS Created page with ''''GWAS''' are genomewide association studies.'
- 15:55, 14 December 2009 diff hist -2 Main Page
- 14:38, 14 December 2009 diff hist +179 N BAM Created page with 'The '''BAM Format''' is a binary format for storing aligned reads. The current definition of the format is at http://samtools.sourceforge.net/SAM1.pdf BAM/SAM Specification…'
- 13:12, 14 December 2009 diff hist +117 N Talk:Examples of Read Mapping with Karma and BWA Created page with 'We need a much more informative title for this page. Also, it needs to linked (in some sensible way) to other pages.'
- 12:37, 14 December 2009 diff hist +1 Examples of Read Mapping with Karma and BWA
- 12:37, 14 December 2009 diff hist +13 Examples of Read Mapping with Karma and BWA
- 12:36, 14 December 2009 diff hist -2 Examples of Read Mapping with Karma and BWA
- 12:36, 14 December 2009 diff hist -6 Examples of Read Mapping with Karma and BWA
- 12:35, 14 December 2009 diff hist +4 SardiNIA →Key References
- 12:35, 14 December 2009 diff hist +142 SardiNIA
- 12:34, 14 December 2009 diff hist +199 SardiNIA
- 12:32, 14 December 2009 diff hist +76 Main Page
- 12:32, 14 December 2009 diff hist +16 SardiNIA →Medical Sequencing Project
- 12:31, 14 December 2009 diff hist +65 SardiNIA
- 12:30, 14 December 2009 diff hist +992 N SardiNIA Created page with '== Key References == If you are looking to learn about the project, I strongly recommend that you read the following papers Pilia G, Chen WM, Scuteri A, Orru M, Albai G, Dei …'
- 15:09, 8 December 2009 diff hist +770 Mantra.cpp current
- 15:02, 8 December 2009 diff hist +1,800 N Mantra.cpp New page: '''Mantra.cpp''' provides useful functions handling inheritance vectors. A call to Mantra::Prepare() will first list all the meioses in a pedigree (which constitute an inheritance vect...
- 03:32, 26 November 2009 diff hist +53 N Utility Library Created page with ' Parameters.h StringHash.h StringMap.h' current
- 03:31, 26 November 2009 diff hist +12 StringMap.h current
- 03:30, 26 November 2009 diff hist +345 N StringMap.h Created page with ''''StringMap.h''' declares classes that allow one to store a list of strings and associated items. The list is stored in sorted fashion. Inserts and deletes can be quite expensiv…'
- 03:26, 26 November 2009 diff hist +224 Parameters.h current
- 03:22, 26 November 2009 diff hist +854 N Parameters.h Created page with '''Parameters.h'' is a header file that defines a series of classes that are useful for processing command line parameters. == Example Usage == <source lang="cpp"> #include "…'
- 11:30, 24 November 2009 diff hist -40 BamGenotypeCheck
- 11:29, 24 November 2009 diff hist +30 N Lanecheck moved Lanecheck to BamIdentityCheck: renamed lane check to bamIdentityCheck which is more descriptive current
- 11:29, 24 November 2009 diff hist 0 m BamGenotypeCheck moved Lanecheck to BamIdentityCheck: renamed lane check to bamIdentityCheck which is more descriptive
- 11:28, 24 November 2009 diff hist -23 TrioCaller Blanked the page
- 14:21, 20 November 2009 diff hist -9 Karma-colorspace →Additional Information
- 14:20, 20 November 2009 diff hist -30 Karma-colorspace
- 14:19, 20 November 2009 diff hist -31 Karma-colorspace →Build Binary Reference Genome and Word Index
- 22:37, 19 November 2009 diff hist +47 Karma
- 17:28, 19 November 2009 diff hist -22 VcfCodingSnps
- 17:27, 19 November 2009 diff hist +90 Main Page →Sequence Analysis Tools
- 17:17, 19 November 2009 diff hist 0 m VcfCodingSnps moved AnnoVcf to VcfCodingSnps: Better name
- 10:06, 18 November 2009 diff hist +64 FastQValidator →Valid FastQ File Requirements
- 10:05, 18 November 2009 diff hist +98 FastQValidator →Valid FastQ File Requirements
- 23:30, 16 November 2009 diff hist +573 N FastQValidator Created page with '== Status == The FastQ Validator is on our Todo List. == Valid FastQ File Requirements == A valid fastQ file should meet the following requirements: * A base sequence sho…'
- 10:43, 16 November 2009 diff hist -1 Karma-colorspace →Input file requirement
- 10:43, 16 November 2009 diff hist -38 Karma-colorspace →Input file requirement
- 10:40, 16 November 2009 diff hist +6 Main Page →Welcome!
- 10:38, 16 November 2009 diff hist +233 Main Page →Welcome!
- 02:10, 15 November 2009 diff hist +1 Main Page →Variant Calling
- 01:52, 15 November 2009 diff hist +190 Abecasis Lab
- 01:49, 15 November 2009 diff hist +1 Abecasis Lab →Former Doctoral Students
- 01:49, 15 November 2009 diff hist +81 Abecasis Lab
- 01:48, 15 November 2009 diff hist +10 Abecasis Lab →Current Members
- 01:47, 15 November 2009 diff hist +831 N Abecasis Lab Created page with '== Current Members == === Research Faculty === Hyun Min Kang === Research Fellows === Bingshan Li === Graduate Students === Wei Chen Jun Ding Youna Hu Elizabeth Jewell Yanm…'
- 01:36, 15 November 2009 diff hist +223 N Genome Analysis Wiki:About Created page with 'This wiki documents useful tools and protocols for genome analysis. It is maintained by the Abecasis Lab at the [http://www.umich.edu University of Michigan] [http://csg.sp…' current
- 01:32, 15 November 2009 diff hist +116 GlfTrio →TODO
- 01:31, 15 November 2009 diff hist +171 GlfSingle
- 01:30, 15 November 2009 diff hist +2,153 N GlfMultiples Created page with ''''glfMultiples''' is a GLF-based variant caller for next-generation sequencing data. It takes a set of GLF format genotype likelihood files as input and generates a [[VC…'
- 00:53, 15 November 2009 diff hist +103 GLF
- 00:51, 15 November 2009 diff hist +10 GlfTrio →Filtering According to Depth and Map Quality
- 00:51, 15 November 2009 diff hist +39 GlfTrio →Basic Usage Example
- 00:48, 15 November 2009 diff hist +152 GlfTrio →Basic Usage Example
- 00:45, 15 November 2009 diff hist 0 GlfTrio →Filtering According to Depth and Map Quality
- 00:45, 15 November 2009 diff hist 0 GlfTrio →Basic Output Options
- 00:44, 15 November 2009 diff hist 0 GlfTrio →X Chromosome Variant Calling
- 00:43, 15 November 2009 diff hist 0 GlfTrio →Sample Labels
- 00:43, 15 November 2009 diff hist -8 GlfTrio →Filtering According to Depth and Map Quality
- 00:43, 15 November 2009 diff hist -8 GlfTrio →Basic Output Options
- 00:42, 15 November 2009 diff hist +2,881 N GlfTrio Created page with ''''glfTrio''' is a GLF-based variant caller for next-generation sequencing data. It takes three GLF format genotype likelihood files as input and generates a VCF-form…'
- 00:04, 15 November 2009 diff hist -2 Main Page →Welcome!
- 19:02, 14 November 2009 diff hist +177 N VCF Created page with ''''VCF''' is the Variant Calling Format. For the current specification, see [http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcfv3.2 VCF format specification].'
- 19:00, 14 November 2009 diff hist +2 Main Page
- 18:59, 14 November 2009 diff hist +278 Main Page
- 18:55, 14 November 2009 diff hist +14 GLF →Last Record
- 18:54, 14 November 2009 diff hist +3,714 GLF
- 18:13, 14 November 2009 diff hist +962 GlfSingle
- 18:07, 14 November 2009 diff hist +556 N GLF Created page with ''''GLF''' is a format for storing marginal likelihoods for next-generation sequence data, conditional on a set of possible genotypes. === Generating GLF Files === GLF files can…'
- 17:59, 14 November 2009 diff hist +448 N GlfSingle Created page with ''''glfSingle''' is a GLF-based variant caller for next-generation sequencing data. It takes a GLF format genotype likelihood file as input and generates a VCF-format …'
- 17:44, 14 November 2009 diff hist +2 METAL Command Reference
- 17:43, 14 November 2009 diff hist +2,100 N METAL Command Reference Created page with '=== Describing Input Files === SEPARATOR [WHITESPACE|COMMA|BOTH|TAB] (default = WHITESPACE) COLUMNCOUNTING [STRICT|LENIENT] (default = 'STRICT') MARK…'
- 01:39, 14 November 2009 diff hist +1 Main Page
- 01:38, 14 November 2009 diff hist +7 Main Page
- 01:37, 14 November 2009 diff hist +2 Main Page
- 01:34, 14 November 2009 diff hist +59 Main Page
- 01:32, 14 November 2009 diff hist +40 N File:2009.08 Group Retreat Photo.jpg Photo from Group Retreat in August 2008.
- 13:52, 13 November 2009 diff hist +48 Karma
- 13:52, 13 November 2009 diff hist +25 N Karma Created page with 'Karma is top secret. Shh!'
- 13:51, 13 November 2009 diff hist +122 Main Page
- 02:19, 11 November 2009 diff hist +3 Main Page
- 02:18, 11 November 2009 diff hist -12 Main Page
- 02:18, 11 November 2009 diff hist -503 Main Page
- 02:17, 11 November 2009 diff hist +78 Main Page
- 02:16, 11 November 2009 diff hist +497 Main Page
- 02:15, 11 November 2009 diff hist +248 Main Page
- 01:38, 11 November 2009 diff hist -31 Main Page
- 01:37, 11 November 2009 diff hist +31 Main Page
- 01:30, 11 November 2009 diff hist 0 Main Page
- 11:52, 10 November 2009 diff hist -423 Main Page