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Jump to navigationJump to search- 18:44, 29 September 2011 diff hist +127 Exome Chip Design →Random set of synonymous variants (as comparator)
- 18:43, 29 September 2011 diff hist -54 Exome Chip Design →Scaffold for Identity by Descent
- 18:42, 29 September 2011 diff hist -17 Exome Chip Design →Native American vs European Ancestry
- 18:39, 29 September 2011 diff hist 0 Exome Chip Design →African American vs European Ancestry
- 18:39, 29 September 2011 diff hist -59 Exome Chip Design →African American vs European Ancestry
- 18:38, 29 September 2011 diff hist -574 Exome Chip Design →Tags for Previously Described GWAS Hits
- 12:59, 29 September 2011 diff hist +77 Exome Chip Design →Additional Content
- 12:58, 29 September 2011 diff hist +432 Exome Chip Design →Variants that Alter Protein Function
- 12:52, 29 September 2011 diff hist +116 Exome Chip Design →Splice Variants
- 12:48, 29 September 2011 diff hist +612 Exome Chip Design →HLA tag SNPs
- 12:42, 29 September 2011 diff hist -358 Exome Chip Design →Variants that Alter Protein Function
- 11:55, 29 September 2011 diff hist +523 Exome Chip Design
- 08:39, 28 September 2011 diff hist +89 Biostatistics 666: Main Page →Scheduling
- 08:35, 28 September 2011 diff hist 0 File:666.04.pdf uploaded a new version of "File:666.04.pdf": Minor typo corrections. current
- 08:34, 28 September 2011 diff hist 0 File:666.05.pdf uploaded a new version of "File:666.05.pdf": Added frequency spectrum from 12,000 individuals. current
- 09:54, 27 September 2011 diff hist -32 Exome Chip Design →Coordination
- 11:24, 22 September 2011 diff hist +113 Abecasis Group Awards →American Society of Human Genetics
- 11:15, 22 September 2011 diff hist +110 Abecasis Group Awards →American Society of Human Genetics
- 00:05, 22 September 2011 diff hist +132 Abecasis Group Awards →American Society of Human Genetics
- 23:47, 21 September 2011 diff hist +344 Minimac Command Reference →Output Parameters
- 23:39, 21 September 2011 diff hist 0 Minimac →Download
- 02:31, 21 September 2011 diff hist +23 Polymutt: a tool for calling polymorphism and de novo mutations in families for sequencing data
- 08:12, 19 September 2011 diff hist +10 Minimac: 1000 Genomes Imputation Cookbook →Imputation into Phased Haplotypes - minimac
- 08:11, 19 September 2011 diff hist +215 Minimac: 1000 Genomes Imputation Cookbook →Imputation into Phased Haplotypes - minimac
- 08:10, 19 September 2011 diff hist +37 Minimac: 1000 Genomes Imputation Cookbook →Further Time Savings
- 08:09, 19 September 2011 diff hist -1 Minimac: 1000 Genomes Imputation Cookbook →Imputation into Phased Haplotypes - minimac
- 08:08, 19 September 2011 diff hist +133 Minimac: 1000 Genomes Imputation Cookbook →Imputation into Phased Haplotypes - minimac
- 07:50, 19 September 2011 diff hist +289 Minimac: 1000 Genomes Imputation Cookbook →Imputation into Phased Haplotypes - minimac
- 07:49, 19 September 2011 diff hist +543 Minimac Command Reference →Reference Haplotype Set
- 07:48, 19 September 2011 diff hist -543 Minimac Command Reference →Target Haplotype Set
- 07:44, 19 September 2011 diff hist +5 Minimac Command Reference →Target Haplotype Set
- 07:44, 19 September 2011 diff hist +6 Minimac Command Reference →Target Haplotype Set
- 07:43, 19 September 2011 diff hist +532 Minimac Command Reference →Target Haplotype Set
- 04:27, 19 September 2011 diff hist -2 Minimac: 1000 Genomes Imputation Cookbook →Questions and Comments
- 04:13, 19 September 2011 diff hist -31 File:666.03.pdf
- 04:12, 19 September 2011 diff hist 0 File:666.03.pdf uploaded a new version of "File:666.03.pdf": →Minor updates to the lecture - added recommended reading list, synchronized content with 2011 lecture series
- 07:33, 12 September 2011 diff hist +348 Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium →Slides current
- 07:32, 12 September 2011 diff hist +48 Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium →Slides
- 07:31, 12 September 2011 diff hist +216 Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium →Objective
- 07:29, 12 September 2011 diff hist +289 N Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium Created page with '== Objective == This lecture does double duty, introducing course objectives and the concept of Hardy Weinberg Equilibrium. It combines topics previously covered in two separat…'
- 07:27, 12 September 2011 diff hist +150 Biostatistics 666: Main Page →Older Lectures
- 07:27, 12 September 2011 diff hist -43 Biostatistics 666: Main Page →Class Notes
- 07:26, 12 September 2011 diff hist +75 N File:2011.666.01.pdf Course Introduction and Hardy Weinberg Lecture Combined into A Single Class
- 05:48, 12 September 2011 diff hist -167 Biostatistics 666: Main Page →Problem Set Solutions
- 05:45, 12 September 2011 diff hist +12 Biostatistics 666: Main Page →Course History
- 05:44, 12 September 2011 diff hist -24 Biostatistics 666: Main Page →Office Hours
- 05:42, 12 September 2011 diff hist -1 Biostatistics 666: Main Page →Scheduling
- 05:42, 12 September 2011 diff hist +65 Biostatistics 666: Main Page →Scheduling
- 05:41, 12 September 2011 diff hist +61 Biostatistics 666: Main Page →Target Audience
- 06:50, 7 September 2011 diff hist -6 Tutorial: Low Pass Sequence Analysis →Converting Alignments to BAM format
- 06:42, 7 September 2011 diff hist -4 Tutorial: Low Pass Sequence Analysis →Browsing Alignment Results
- 06:42, 7 September 2011 diff hist -4 Tutorial: Low Pass Sequence Analysis →Indexing the BAM file
- 06:41, 7 September 2011 diff hist +5 Tutorial: Low Pass Sequence Analysis →Converting Alignments to BAM format
- 06:38, 7 September 2011 diff hist -4 Tutorial: Low Pass Sequence Analysis →Converting Alignments to BAM format
- 06:36, 7 September 2011 diff hist +27 Tutorial: Low Pass Sequence Analysis →Browsing Alignment Results
- 06:29, 7 September 2011 diff hist +5 Tutorial: Low Pass Sequence Analysis →Browsing Alignment Results
- 06:28, 7 September 2011 diff hist -1 Tutorial: Low Pass Sequence Analysis →Mapping Reads to The Genome
- 05:47, 7 September 2011 diff hist -1 Tutorial: Low Pass Sequence Analysis →Initial set of variant calls
- 05:36, 7 September 2011 diff hist +7 Tutorial: Low Pass Sequence Analysis →Initial set of variant calls
- 05:35, 7 September 2011 diff hist -5 Tutorial: Low Pass Sequence Analysis →Converting Alignments to BAM format
- 05:35, 7 September 2011 diff hist -4 Tutorial: Low Pass Sequence Analysis →Indexing and Annotating the BAM file
- 05:18, 7 September 2011 diff hist +1,593 Tutorial: Low Pass Sequence Analysis →Mapping Reads to The Genome
- 04:55, 7 September 2011 diff hist +1,940 Tutorial: Low Pass Sequence Analysis →Initial set of variant calls
- 04:37, 7 September 2011 diff hist +1 Tutorial: Low Pass Sequence Analysis →Mapping Reads to The Genome
- 04:35, 7 September 2011 diff hist -3 Tutorial: Low Pass Sequence Analysis →Sequence Analysis Workshop
- 04:32, 7 September 2011 diff hist +4,561 N Tutorial: Low Pass Sequence Analysis Created page with '= Sequence Analysis Workshop = In this workshop, we will illustrate some of the essential steps in the analysis of next generation sequence data. As part of the process, you wil…'
- 04:27, 7 September 2011 diff hist +42 Short Workshops
- 06:14, 2 September 2011 diff hist 0 Minimac →Download
- 11:19, 23 August 2011 diff hist +47 Exome Chip Design →Ancestry Informative Markers
- 11:18, 23 August 2011 diff hist +54 Exome Chip Design →Scaffold for Identity by Descent
- 11:16, 23 August 2011 diff hist +50 Exome Chip Design →Random set of synonymous variants (as comparator)
- 11:06, 23 August 2011 diff hist +59 Exome Chip Design →Ancestry Informative Markers
- 10:01, 23 August 2011 diff hist +154 Exome Chip Design →Tags for Previously Described GWAS Hits
- 09:56, 23 August 2011 diff hist -3 Exome Chip Design →Variants that Alter Protein Function
- 09:56, 23 August 2011 diff hist +2 Exome Chip Design →Variants that Alter Protein Function
- 09:55, 23 August 2011 diff hist +217 Exome Chip Design →Ancestry Informative Markers
- 09:46, 23 August 2011 diff hist 0 Exome Chip Design →Fingerprint SNPs
- 09:44, 23 August 2011 diff hist +143 Exome Chip Design →HLA tag SNPs
- 09:42, 23 August 2011 diff hist +57 Exome Chip Design →Fingerprint SNPs
- 22:09, 18 August 2011 diff hist 0 Minimac →Download
- 23:07, 16 August 2011 diff hist +8,205 N Exome Chip Design Created page with 'This page describes characteristics of the Illumina Exome Chip. The plan is that this page will be publicly visible. = Key Credit = We thank all the individuals who generously …'
- 06:47, 12 August 2011 diff hist -1 Minimac →Additional Sources of Information
- 06:46, 12 August 2011 diff hist 0 Minimac →Download
- 16:24, 10 August 2011 diff hist +336 IMPUTE2: 1000 Genomes Imputation Cookbook →Association Analysis
- 16:19, 10 August 2011 diff hist +138 IMPUTE2: 1000 Genomes Imputation Cookbook →Pre-Phasing using IMPUTE2
- 16:17, 10 August 2011 diff hist +76 IMPUTE2 current
- 15:13, 5 August 2011 diff hist +1 Minimac →Additional Sources of Information
- 11:15, 5 August 2011 diff hist +504 Minimac →Getting Started
- 11:10, 5 August 2011 diff hist +48 Minimac →Download
- 11:09, 5 August 2011 diff hist -2 Minimac →X Chromosome Imputation
- 10:12, 5 August 2011 diff hist -222 Minimac →NCBI build 36 / NCBI build 37
- 10:12, 5 August 2011 diff hist +748 Minimac: 1000 Genomes Imputation Cookbook →Further Time Savings
- 10:06, 5 August 2011 diff hist +43 Minimac: 1000 Genomes Imputation Cookbook →Further Time Savings
- 10:05, 5 August 2011 diff hist +1,596 Minimac: 1000 Genomes Imputation Cookbook →Further Time Savings
- 10:05, 5 August 2011 diff hist -16 ChunkChromosome →Usage
- 09:14, 5 August 2011 diff hist +359 Minimac: 1000 Genomes Imputation Cookbook
- 09:02, 5 August 2011 diff hist +287 Minimac: 1000 Genomes Imputation Cookbook →Your Own Data
- 08:55, 5 August 2011 diff hist +42 ChunkChromosome →Download
- 08:55, 5 August 2011 diff hist +102 ChunkChromosome →Download
- 08:52, 5 August 2011 diff hist +114 Minimac →Download
- 08:40, 5 August 2011 diff hist +150 ChunkChromosome →Download
- 08:06, 5 August 2011 diff hist +5 ChunkChromosome →Usage
- 08:05, 5 August 2011 diff hist +376 ChunkChromosome →Usage
- 07:55, 5 August 2011 diff hist +439 ChunkChromosome →Usage
- 07:43, 5 August 2011 diff hist +393 ChunkChromosome →Usage
- 07:26, 5 August 2011 diff hist +23 ChunkChromosome →Usage
- 07:23, 5 August 2011 diff hist 0 ChunkChromosome →Usage
- 07:22, 5 August 2011 diff hist +1,171 N ChunkChromosome Created page with '''ChunkChromosome'' is a helper utility for minimac and MaCH. It can be used to facilitate analyses of very large datasets in overlapping slices. == Parameters == ''Chu…'
- 07:12, 5 August 2011 diff hist +841 N Hardy Weinberg equilibrium Created page with 'In the absence of migration, mutation, natural selection, and assortative mating, genotype frequencies at any locus are a simple function of allele frequencies. This phenomenon, …' current
- 07:07, 5 August 2011 diff hist +1 Minimac: 1000 Genomes Imputation Cookbook →Shoud I use MaCH or minimac?
- 07:02, 5 August 2011 diff hist +44 Minimac: 1000 Genomes Imputation Cookbook →X Chromosome Imputation
- 07:00, 5 August 2011 diff hist +14 Minimac: 1000 Genomes Imputation Cookbook →Imputation quality evaluation
- 06:59, 5 August 2011 diff hist -3 Minimac: 1000 Genomes Imputation Cookbook →X Chromosome Imputation
- 06:57, 5 August 2011 diff hist +269 Minimac: 1000 Genomes Imputation Cookbook →Reference Haplotypes
- 06:54, 5 August 2011 diff hist +591 Minimac: 1000 Genomes Imputation Cookbook →Your Own Data
- 06:49, 5 August 2011 diff hist +69 N IMPUTE2 Created page with 'An imputation package developed by Bryan Howie and Jonathan Marchini.'
- 06:48, 5 August 2011 diff hist +189 IMPUTE2: 1000 Genomes Imputation Cookbook →Content
- 06:47, 5 August 2011 diff hist +127 Minimac: 1000 Genomes Imputation Cookbook
- 06:43, 5 August 2011 diff hist +391 IMPUTE2: 1000 Genomes Imputation Cookbook →Content
- 06:40, 5 August 2011 diff hist +82 IMPUTE2: 1000 Genomes Imputation Cookbook →Imputation
- 06:40, 5 August 2011 diff hist -1 IMPUTE2: 1000 Genomes Imputation Cookbook →Association Analysis =
- 06:39, 5 August 2011 diff hist +50 IMPUTE2: 1000 Genomes Imputation Cookbook →Imputation
- 06:37, 5 August 2011 diff hist +1 IMPUTE2: 1000 Genomes Imputation Cookbook →Pre-Phasing using IMPUTE2
- 06:36, 5 August 2011 diff hist -3 IMPUTE2: 1000 Genomes Imputation Cookbook →Pre-Phasing using IMPUTE2 =
- 06:35, 5 August 2011 diff hist -1,210 IMPUTE2: 1000 Genomes Imputation Cookbook →Pre-Phasing using IMPUTE2 =
- 06:16, 5 August 2011 diff hist +2 IMPUTE2: 1000 Genomes Imputation Cookbook →Pre-Phasing using IMPUTE2 =
- 06:15, 5 August 2011 diff hist -4 IMPUTE2: 1000 Genomes Imputation Cookbook →Pre-Phasing using IMPUTE2 =
- 06:15, 5 August 2011 diff hist -2 IMPUTE2: 1000 Genomes Imputation Cookbook →Pre-Phasing using IMPUTE2 =
- 06:14, 5 August 2011 diff hist +8,254 IMPUTE2: 1000 Genomes Imputation Cookbook →Pre-Phasing
- 05:38, 5 August 2011 diff hist +54 IMPUTE2: 1000 Genomes Imputation Cookbook →Content
- 05:38, 5 August 2011 diff hist +499 IMPUTE2: 1000 Genomes Imputation Cookbook →Convert Genotype Data to Build 37
- 05:31, 5 August 2011 diff hist -3 IMPUTE2: 1000 Genomes Imputation Cookbook →Convert Genotype Data to Build 37
- 05:31, 5 August 2011 diff hist +1,441 IMPUTE2: 1000 Genomes Imputation Cookbook →Convert Genotype Data to Build 37
- 05:21, 5 August 2011 diff hist +1,329 N IMPUTE2: 1000 Genomes Imputation Cookbook Created page with '= Introduction = == Authors == This page is based on a document prepared by Jian'an Luan, Alexander Teumer, Jing-Hua Zhao, Christian Fuchsberger and Cristen Willer for the GIAN…'
- 03:29, 28 July 2011 diff hist -1,671 Minimac: 1000 Genomes Imputation Cookbook
- 03:08, 28 July 2011 diff hist +461 MaCH: 1000 Genomes Imputation Cookbook current
- 03:02, 28 July 2011 diff hist +55 N 1000G Cookbook moved 1000G Cookbook to Minimac: 1000 Genomes Imputation Cookbook: Switched to more informative title current
- 03:02, 28 July 2011 diff hist 0 m Minimac: 1000 Genomes Imputation Cookbook moved 1000G Cookbook to Minimac: 1000 Genomes Imputation Cookbook: Switched to more informative title
- 14:54, 21 July 2011 diff hist +1 Bar Harbor Statistical Genetics Workshop →Web Resources current
- 14:53, 21 July 2011 diff hist 0 Bar Harbor Statistical Genetics Workshop →Web Resources
- 13:47, 21 July 2011 diff hist +583 Bar Harbor Statistical Genetics Workshop →Questions to Consider
- 13:36, 21 July 2011 diff hist 0 Bar Harbor Statistical Genetics Workshop →Glusose Data Set
- 20:32, 24 June 2011 diff hist +12 Abecasis Lab →Staff
- 20:31, 24 June 2011 diff hist +18 Abecasis Lab →Graduate Students
- 20:27, 24 June 2011 diff hist +18 Abecasis Lab →Former Masters Students
- 20:26, 24 June 2011 diff hist -18 Abecasis Lab →Graduate Students
- 20:26, 24 June 2011 diff hist +10 Abecasis Lab →Former Masters Students
- 20:21, 24 June 2011 diff hist -4 Abecasis Lab →Staff
- 20:21, 24 June 2011 diff hist +20 Abecasis Lab →International Visitors
- 20:21, 24 June 2011 diff hist +25 Abecasis Lab →Research Fellows
- 20:20, 24 June 2011 diff hist +217 Abecasis Lab →Alumni
- 20:19, 24 June 2011 diff hist -41 Abecasis Lab →Current Members
- 20:18, 24 June 2011 diff hist +47 MediaWiki:Sidebar
- 20:17, 24 June 2011 diff hist +46 N 815 Redirected page to Biostatistics 615/815: Main Page current
- 20:16, 24 June 2011 diff hist +2 615 Redirected page to Biostatistics 615/815: Main Page current
- 20:16, 24 June 2011 diff hist +44 N 615 Created page with '#REDIRECT [Biostatistics 615/815: Main Page]'
- 20:15, 24 June 2011 diff hist +1 Class Notes
- 20:14, 24 June 2011 diff hist +99 Class Notes
- 20:13, 24 June 2011 diff hist +399 Class Notes →BIOSTAT 615 / 815 Statistical Computing
- 20:11, 24 June 2011 diff hist +84 Class Notes →BIOSTAT 666 Statistical and Numerical Methods in Human Genetics
- 02:55, 20 June 2011 diff hist +15 Abecasis Lab →Former Masters Students
- 07:48, 10 June 2011 diff hist +231 Nm User talk:Feng Zhang Welcome! current
- 07:48, 10 June 2011 diff hist +336 Nm User:Feng Zhang Creating user page with biography of new user. current
- 06:41, 26 April 2011 diff hist +328 Minimac →Imputation into Phased Haplotypes
- 06:36, 26 April 2011 diff hist +61 Minimac →Pre-phasing
- 06:18, 26 April 2011 diff hist -1 Minimac: 1000 Genomes Imputation Cookbook →Selecting a Subset of Samples
- 06:17, 26 April 2011 diff hist +51 Minimac: 1000 Genomes Imputation Cookbook →Shoud I use MaCH or minimac?
- 04:56, 26 April 2011 diff hist +97 Minimac: 1000 Genomes Imputation Cookbook →Quality Control
- 07:19, 8 April 2011 diff hist +23 Minimac: 1000 Genomes Imputation Cookbook →Quality Control
- 07:11, 8 April 2011 diff hist +613 Minimac: 1000 Genomes Imputation Cookbook →Your Own Data
- 07:07, 8 April 2011 diff hist 0 Minimac: 1000 Genomes Imputation Cookbook →Your Own Data
- 07:06, 8 April 2011 diff hist +74 Minimac: 1000 Genomes Imputation Cookbook →Shoud I use MaCH or minimac?
- 10:33, 25 March 2011 diff hist +119 METAL current
- 09:43, 25 March 2011 diff hist +2 METAL Documentation →History
- 09:43, 25 March 2011 diff hist +117 METAL Documentation →History
- 07:36, 25 March 2011 diff hist 0 METAL Command Reference →Genomic Control Correction of Input Statistics current
- 07:34, 25 March 2011 diff hist +891 METAL GENOMICCONTROL current
- 17:57, 10 March 2011 diff hist 0 Minimac →post-imputation association analysis
- 17:55, 10 March 2011 diff hist -10 Minimac →binary traits
- 17:55, 10 March 2011 diff hist +5 Minimac →X Chromosome Imputation
- 17:54, 10 March 2011 diff hist +155 Minimac →Imputation into Phased Haplotypes
- 17:51, 10 March 2011 diff hist +82 Minimac →NCBI build 36 / NCBI build 37
- 17:47, 10 March 2011 diff hist +3 Minimac →Imputation
- 17:46, 10 March 2011 diff hist +334 Minimac →Pre-phasing
- 17:58, 7 February 2011 diff hist -23 Rare variant tests →Summary of rare variant tests for sequence data
- 06:03, 22 January 2011 diff hist -104 Abecasis Group Awards →American Society of Human Genetics
- 05:50, 22 January 2011 diff hist +104 Abecasis Group Awards →American Society of Human Genetics
- 05:46, 22 January 2011 diff hist +2 Abecasis Group Awards →American Society of Human Genetics
- 12:43, 6 January 2011 diff hist -10 Abecasis Lab →Graduate Students
- 12:42, 6 January 2011 diff hist +177 Abecasis Lab →Former Doctoral Students
- 21:05, 2 December 2010 diff hist +246 N Biostatistics 666: Copy Number Variation Created page with '== Overview == Introduces the analysis of copy number variation. Principles behind the detection of copy number variation with binary segmentation models and hidden markov model…' current
- 21:03, 2 December 2010 diff hist +82 Biostatistics 666: Main Page →Class Notes
- 21:02, 2 December 2010 diff hist +60 N File:666.Zollner.CNV.pdf Guest lecture by Sebastian Zollner on Copy Number Variation. current
- 23:39, 1 December 2010 diff hist 0 N File:666.2010.05.pdf
- 23:32, 1 December 2010 diff hist +721 N Biostatistics 666: Analysis of Low Pass Sequence Data Created page with '== Objective == Discussion of the challenges involved in sequencing thousands of individual genomes. Introduction to the analysis of low pass sequence data. == Lecture Notes ==…' current
- 23:30, 1 December 2010 diff hist +91 Biostatistics 666: Main Page →Class Notes
- 15:57, 29 November 2010 diff hist +172 Biostatistics 666: Main Page →Older Lectures
- 15:57, 29 November 2010 diff hist -167 Biostatistics 666: Main Page →Class Notes
- 15:56, 29 November 2010 diff hist +160 Biostatistics 666: Whole Genome Sequencing →Lecture Notes
- 15:55, 29 November 2010 diff hist +98 N File:666.2010.04.pdf Basic introduction to some of the issues and opportunities posed by whole genome sequence studies.
- 04:32, 29 November 2010 diff hist +67 Minimac →Download
- 04:31, 29 November 2010 diff hist +66 Minimac Undo revision 2568 by Cfuchsb (Talk)
- 04:30, 29 November 2010 diff hist -25 Minimac Undo revision 2569 by Cfuchsb (Talk)
- 19:10, 24 November 2010 diff hist 0 File:666.2010.03.pdf uploaded a new version of "File:666.2010.03.pdf"
- 07:21, 23 November 2010 diff hist +62 N Talk:Examples moved Talk:Examples to Talk:Examples of Read Mapping with Karma and BWA current
- 07:21, 23 November 2010 diff hist 0 m Talk:Examples of Read Mapping with Karma and BWA moved Talk:Examples to Talk:Examples of Read Mapping with Karma and BWA current
- 07:21, 23 November 2010 diff hist +57 N Examples moved Examples to Examples of Read Mapping with Karma and BWA current
- 07:21, 23 November 2010 diff hist 0 m Examples of Read Mapping with Karma and BWA moved Examples to Examples of Read Mapping with Karma and BWA
- 07:18, 23 November 2010 diff hist +596 N Biostatistics 666: Genotype Imputation Created page with '== Overview == Genotype imputation is one of the most commonly used tools for the analysis of genomewide association studies. This lecture introduces the basic ideas behind geno…'
- 07:15, 23 November 2010 diff hist +76 Biostatistics 666: Main Page →Class Notes
- 07:14, 23 November 2010 diff hist +116 N File:666.2010.03.pdf Introduction to Genotype Imputation, describes imputation in families and later in samples of unrelated individuals.
- 04:17, 23 November 2010 diff hist +4 RelativeFinder →Current Limitations and Todo List current
- 03:47, 18 November 2010 diff hist 0 File:666.17.pdf uploaded a new version of "File:666.17.pdf": Minor refinements to axis.
- 08:59, 16 November 2010 diff hist 0 File:666.2010.02.pdf uploaded a new version of "File:666.2010.02.pdf": Fixes minor errors.
- 08:59, 16 November 2010 diff hist 0 File:666.16.pdf uploaded a new version of "File:666.16.pdf": Updated version of lecture with more detailed review of ASP analysis
- 13:19, 12 November 2010 diff hist +32 N User talk:Goncalo Created page with 'Is there anything to talk about?' current
- 03:08, 11 November 2010 diff hist +6 Biostatistics 666: Linkage Analysis in Sibling Pairs →Slides
- 03:08, 11 November 2010 diff hist +665 N Biostatistics 666: Linkage Analysis in Sibling Pairs Created page with '== Outline == This lecture introduces Neil Risch's Maximum Lod Score (MLS) test for linkage and its refinement using Peter Holman's possible triangle constraint. == Slides == …'
- 03:02, 11 November 2010 diff hist +222 Biostatistics 666: Main Page →Class Notes
- 02:59, 11 November 2010 diff hist +62 N File:666.2010.02.pdf Lecture describing Risch's MLS and Holman's Possible Triangle.
- 16:12, 10 November 2010 diff hist -1 Minimac →Download
- 11:07, 9 November 2010 diff hist 0 File:666.2010.01.pdf uploaded a new version of "File:666.2010.01.pdf": Lecture on power calculation for genomewide association studies. Also introduces the idea of two stage genomewide association studies. ** Lots of typos fixed in this version ** current
- 06:23, 9 November 2010 diff hist +6 Biostatistics 666: Power of Genomewide Association Studies →Lecture Notes
- 06:23, 9 November 2010 diff hist +541 N Biostatistics 666: Power of Genomewide Association Studies Created page with '== Objective == This lecture discusses power calculations in the context of genomewide association studies. It also introduces the concept of two stage designs and the tradeoffs…'
- 06:19, 9 November 2010 diff hist 0 N File:666.2010.01.pdf
- 06:18, 9 November 2010 diff hist +95 Biostatistics 666: Main Page →Class Notes
- 10:23, 28 October 2010 diff hist 0 File:666.20.pdf uploaded a new version of "File:666.20.pdf": Fixed a small typo. Compared to original version, this one also includes slightly more informative titles.
- 08:14, 28 October 2010 diff hist 0 File:666.20.pdf uploaded a new version of "File:666.20.pdf": Minor update to include kinship coefficients.
- 04:30, 26 October 2010 diff hist +237 Biostatistics 666: Association Tests in Structured Populations →Overview current
- 04:28, 26 October 2010 diff hist +82 Biostatistics 666: Association Tests in Structured Populations →Recommended Reading
- 04:27, 26 October 2010 diff hist 0 File:666.13.pdf uploaded a new version of "File:666.13.pdf": Added a summary slide at the beginning. current
- 04:18, 26 October 2010 diff hist 0 File:666.13.pdf uploaded a new version of "File:666.13.pdf": Updated lecture to include QQ plots, brief mention of principal component analysis.
- 15:05, 25 October 2010 diff hist +244 Abecasis Group Awards →American Society of Human Genetics
- 15:22, 22 October 2010 diff hist +2 Genotype Likelihood Based Allele Balance →Calculation current
- 15:21, 22 October 2010 diff hist +20 Genotype Likelihood Based Allele Balance →Calculation
- 15:19, 22 October 2010 diff hist -5 Genotype Likelihood Based Allele Balance →Calculation
- 15:18, 22 October 2010 diff hist -1 Genotype Likelihood Based Allele Balance →Calculation
- 15:18, 22 October 2010 diff hist +97 Genotype Likelihood Based Allele Balance →Inputs
- 15:17, 22 October 2010 diff hist +513 N Genotype Likelihood Based Allele Balance Created page with 'A statistic developed by Dr. Tom Blackwell. == Inputs == ; '''depth''' : at each site ; lrr : phred-scaled likelihood of observed bases given reference genotype ; lsr : phr…'
- 09:59, 21 October 2010 diff hist +341 Minimac Diagnostics →Basic Descriptors
- 09:55, 21 October 2010 diff hist +1,160 N Minimac Diagnostics Created page with ''''minimac''' is a tool for imputation of missing genotypes into phased haplotypes. At the end of each run, minimac generates summaries of imputation quality and stores t…'
- 09:49, 18 October 2010 diff hist +46 Biostatistics 666: Main Page →Problem Set Solutions
- 19:13, 12 October 2010 diff hist +3 Minimac →Running Minimac
- 19:13, 12 October 2010 diff hist +13 Minimac →Running MaCH
- 19:01, 12 October 2010 diff hist 0 File:666.12.pdf uploaded a new version of "File:666.12.pdf": Typo fixes.
- 07:58, 12 October 2010 diff hist 0 File:666.12.pdf uploaded a new version of "File:666.12.pdf": Minor update.
- 04:06, 12 October 2010 diff hist 0 Minimac
- 04:05, 12 October 2010 diff hist +54 Minimac →Questions and Comments
- 04:03, 12 October 2010 diff hist +89 Minimac →Multiprocessor Version
- 04:02, 12 October 2010 diff hist -2 Minimac →Download
- 04:01, 12 October 2010 diff hist +615 Minimac →Download
- 03:55, 12 October 2010 diff hist -2 Minimac →Related Pages
- 03:54, 12 October 2010 diff hist +6 Minimac →Your Own Data
- 03:53, 12 October 2010 diff hist +18 Minimac →Running Minimac
- 03:51, 12 October 2010 diff hist -14 Minimac →Getting Started
- 03:51, 12 October 2010 diff hist -6 Minimac →Release Date
- 03:50, 12 October 2010 diff hist -2 Minimac →Performance
- 03:50, 12 October 2010 diff hist +16 Minimac →Running Minimac
- 03:48, 12 October 2010 diff hist +1,307 Minimac →Getting Started
- 03:36, 12 October 2010 diff hist +24 Minimac
- 03:34, 12 October 2010 diff hist -73 Minimac →Parameters
- 03:32, 12 October 2010 diff hist +399 Minimac →Parameters
- 03:24, 12 October 2010 diff hist +39 Minimac →Parameters
- 03:22, 12 October 2010 diff hist +45 Minimac →Parameters
- 03:20, 12 October 2010 diff hist -10 Minimac →Parameters
- 03:19, 12 October 2010 diff hist +12 Minimac →Parameters
- 00:34, 12 October 2010 diff hist +3 Biostatistics 666: Haplotype Association Tests →Objective current
- 00:33, 12 October 2010 diff hist +2 Biostatistics 666: Haplotype Association Tests →Recommended Reading
- 00:33, 12 October 2010 diff hist -2 Biostatistics 666: Haplotype Association Tests →Recommended Reading
- 00:32, 12 October 2010 diff hist +176 Biostatistics 666: Haplotype Association Tests →Recommended Reading
- 22:31, 7 October 2010 diff hist +2,102 N Minimac Command Reference Created page with 'Minimac runs are controled by a series of command line parameters that specify input file names, an initial model for recombination and error rates, an optional series of ite…'
- 12:11, 7 October 2010 diff hist +475 Minimac →Performance
- 08:57, 7 October 2010 diff hist +99 Biostatistics 666: Main Page →Scheduling
- 04:03, 7 October 2010 diff hist +180 Biostatistics 666: Main Page →Scheduling
- 03:54, 7 October 2010 diff hist +1 Biostatistics 666: Introduction to the E-M Algorithm →Slides
- 03:53, 7 October 2010 diff hist 0 File:666.11.pdf uploaded a new version of "File:666.11.pdf": Minor typos fixed. current
- 02:01, 7 October 2010 diff hist +63 Abecasis Group Awards →Goncalo's Awards
- 02:00, 7 October 2010 diff hist +127 Abecasis Group Awards →European Society of Human Genetics
- 01:58, 7 October 2010 diff hist +150 Abecasis Group Awards →American Society of Human Genetics
- 01:51, 5 October 2010 diff hist 0 File:666.09.pdf uploaded a new version of "File:666.09.pdf": Fixes several typos. current
- 01:51, 5 October 2010 diff hist 0 File:666.09.Master.pdf uploaded a new version of "File:666.09.Master.pdf": Minor clarification of different uses of N. current
- 10:10, 4 October 2010 diff hist 0 Minimac →Your Own Data
- 10:07, 4 October 2010 diff hist +2 Minimac →Your Own Data
- 09:57, 4 October 2010 diff hist -125 Biostatistics 666: Main Page →Problem Set Solutions
- 09:56, 4 October 2010 diff hist -2 Biostatistics 666: Main Page →Problem Set Solutions
- 03:47, 3 October 2010 diff hist +1 Fst →Formulae current
- 03:46, 3 October 2010 diff hist +7 Fst →Formulae
- 03:46, 3 October 2010 diff hist +175 Fst →Formulae
- 03:41, 3 October 2010 diff hist +163 Fst
- 03:39, 3 October 2010 diff hist +453 N Fst Created page with ''''F<sub>st</sub>''' is a measure of population divergence. It measures the reduction in heterozygosity in a subdivided population compared to that in large, random mating popula…'
- 15:10, 30 September 2010 diff hist -103 Biostatistics 666: Haplotype Estimation Undo revision 2129 by Goncalo (Talk)
- 15:09, 30 September 2010 diff hist +103 Biostatistics 666: Haplotype Estimation
- 13:03, 30 September 2010 diff hist -1 Minimac
- 13:01, 30 September 2010 diff hist -3 Minimac →Performance
- 13:00, 30 September 2010 diff hist -12 Minimac →Performance
- 12:53, 30 September 2010 diff hist +10 Minimac →Performance
- 12:52, 30 September 2010 diff hist +689 Minimac
- 08:35, 30 September 2010 diff hist +7 Biostatistics 666: Maximum Likelihood Allele Frequency Estimation →Slides
- 08:29, 30 September 2010 diff hist +166 Biostatistics 666: Maximum Likelihood Allele Frequency Estimation →Slides
- 08:28, 30 September 2010 diff hist +102 N File:666.09.Master.pdf Lecturer's slides for lecture on allele frequency estimation. Include solutions to in class exercises.
- 23:47, 29 September 2010 diff hist +36 Tramp →Where to get it current
- 08:44, 28 September 2010 diff hist 0 File:666.06.pdf uploaded a new version of "File:666.06.pdf"
- 20:04, 27 September 2010 diff hist +1,210 Biostatistics 666: Introduction to the Coalescent →Objective
- 13:33, 27 September 2010 diff hist -40 m SNP Call Set Properties Reverted edits by Mertcenk11 (Talk) to last revision by Goncalo
- 13:32, 27 September 2010 diff hist +8 Zlib
- 13:27, 27 September 2010 diff hist +794 N Zlib Created page with 'The '''zlib''' allows applications to conveniently read and write gzip compatible files. It was developed by Jean-Loupe Gailly and Mark Adler. == Linux == '''zlib''' is inc…'
- 12:48, 27 September 2010 diff hist +662 New Fugue →Download
- 14:04, 24 September 2010 diff hist +141 Tramp
- 11:33, 23 September 2010 diff hist +7 Minimac →Related Pages
- 14:43, 22 September 2010 diff hist -28 MaCH FAQ →How is AL1 defined? Which allele dosage is .dose/.mldose counting?
- 14:42, 22 September 2010 diff hist -23 MaCH FAQ →More questions?
- 14:42, 22 September 2010 diff hist +23 MaCH
- 14:41, 22 September 2010 diff hist +984 N Minimac Created page with ''''minimac''' is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle v…'
- 07:52, 21 September 2010 diff hist +12 Biostatistics 666: Main Page →Course History
- 07:51, 21 September 2010 diff hist +421 Biostatistics 666: Introduction to the Coalescent →Objective
- 01:50, 21 September 2010 diff hist 0 File:666.04.pdf uploaded a new version of "File:666.04.pdf": Minor typos fixed.
- 09:50, 16 September 2010 diff hist +2 Biostatistics 666: Main Page →Office Hours
- 23:33, 15 September 2010 diff hist 0 File:666.04.pdf uploaded a new version of "File:666.04.pdf": Introductory lecture on the coalescent. This version fixes some minor typos.
- 14:33, 14 September 2010 diff hist +910 N NHLBI Exome Sequencing Project Created page with 'The '''NHLBI Exome Sequencing Project''' is using deep whole exome resequencing of >7,000 individuals to study genetic contributions to the risk of several heart, lung and blood …'
- 08:45, 14 September 2010 diff hist +92 Biostatistics 666: Main Page →Office Hours
- 02:25, 14 September 2010 diff hist 0 File:666.03.pdf uploaded a new version of "File:666.03.pdf"
- 02:24, 14 September 2010 diff hist 0 File:666.02.pdf uploaded a new version of "File:666.02.pdf" current
- 02:03, 14 September 2010 diff hist +75 Biostatistics 666: Linkage Disequilibrium →Background Reading
- 02:02, 14 September 2010 diff hist -12 Biostatistics 666: Linkage Disequilibrium
- 02:01, 14 September 2010 diff hist +384 Biostatistics 666: Linkage Disequilibrium →Objective
- 01:05, 9 September 2010 diff hist -1 Abecasis Lab →Former Research Fellows
- 23:21, 8 September 2010 diff hist +49 Main Page →High Level Tutorials
- 23:20, 8 September 2010 diff hist +6,058 N Talk:Evaluating a Read Mapper on Simulated Data Created page with 'This stuff was originally included in the main page, but seems pretty specific to our local uses, so I have moved it here, to the talk page. Probably even better to go into our i…' current
- 23:19, 8 September 2010 diff hist -5,867 Evaluating a Read Mapper on Simulated Data current
- 23:18, 8 September 2010 diff hist +14 Gzip
- 23:16, 8 September 2010 diff hist +39 Gzip File current
- 23:15, 8 September 2010 diff hist -14 Gzip
- 23:15, 8 September 2010 diff hist +2 Gzip
- 23:14, 8 September 2010 diff hist +12 Gzip
- 23:13, 8 September 2010 diff hist +162 Abecasis Lab →Mission Statement
- 23:11, 8 September 2010 diff hist +170 Main Page →Sequence Analysis Tools
- 23:08, 8 September 2010 diff hist 0 Main Page →Abecasis Group Meeting
- 23:07, 8 September 2010 diff hist -30 Main Page →Sequence Analysis Tools
- 23:07, 8 September 2010 diff hist +5 SNP Call Set Properties →Proportion of dbSNPs
- 23:06, 8 September 2010 diff hist -2 SNP Call Set Properties →Why Are Reciprocal Changes Not Equally Frequent?
- 23:06, 8 September 2010 diff hist +3,253 N SNP Call Set Properties Created page with 'There are typically a number of properties that we check in SNP call sets. This page gives some useful pointers on what these quantities are and what to look for. == Proportion …'
- 22:37, 8 September 2010 diff hist +84 Biostatistics 666: Hardy-Weinberg Equilibrium →Background Reading
- 22:34, 8 September 2010 diff hist 0 File:666.02.pdf uploaded a new version of "File:666.02.pdf"
- 10:14, 7 September 2010 diff hist +421 Biostatistics 666: Introductory Lecture current
- 08:54, 7 September 2010 diff hist +12 Biostatistics 666: Main Page →Target Audience
- 06:01, 7 September 2010 diff hist +91 Biostatistics 666: Introductory Lecture →Objective
- 05:59, 7 September 2010 diff hist -5 Biostatistics 666: Introductory Lecture →Objective
- 05:58, 7 September 2010 diff hist +6 Biostatistics 666: Introductory Lecture →Objective
- 05:57, 7 September 2010 diff hist +1,846 Biostatistics 666: Introductory Lecture →Objective
- 05:46, 7 September 2010 diff hist 0 File:666.01.pdf uploaded a new version of "File:666.01.pdf": Biostatistics 666 Introductory Lecture as of 2010/09/07 current
- 22:53, 2 September 2010 diff hist +30 Biostatistics 666: Main Page →Office Hours
- 22:45, 2 September 2010 diff hist -135 Biostatistics 666: Main Page →Scheduling
- 11:49, 25 August 2010 diff hist +129 Abecasis Group Awards →Goncalo's Awards
- 11:47, 25 August 2010 diff hist +288 Abecasis Group Awards →American Society of Human Genetics
- 16:54, 20 August 2010 diff hist +87 Abecasis Group Awards →American Society of Human Genetics
- 16:53, 20 August 2010 diff hist +334 N Abecasis Group Awards Created page with 'This is a record of awards won by group members. == American Society of Human Genetics == * Paul Scheet, Cotterman Award, American Society of Human Genetics 2006 * Yun Li, Pred…'
- 16:44, 20 August 2010 diff hist +30 Abecasis Lab →Really Useful Stuff
- 16:37, 17 August 2010 diff hist -2 Abecasis Lab →Really Useful Stuff
- 16:37, 17 August 2010 diff hist +70 Abecasis Lab →Really Useful Stuff
- 16:20, 17 August 2010 diff hist +83 Abecasis Lab
- 01:27, 14 August 2010 diff hist +26 GlfTrio →X Chromosome Variant Calling
- 01:26, 14 August 2010 diff hist +198 GlfTrio →X Chromosome Variant Calling
- 15:42, 13 August 2010 diff hist +43 Abecasis Lab →Graduate Students
- 13:18, 13 August 2010 diff hist -206 RelativeFinder →Current Limitations and Todo List
- 13:18, 13 August 2010 diff hist 0 RelativeFinder →Download
- 17:08, 12 August 2010 diff hist +178 RelativeFinder →Command Line Options
- 17:07, 12 August 2010 diff hist 0 RelativeFinder →Download
- 17:06, 12 August 2010 diff hist +694 RelativeFinder →Alternative Relationships
- 14:58, 22 July 2010 diff hist 0 Bar Harbor Statistical Genetics Workshop →Your Tasks
- 13:47, 22 July 2010 diff hist +129 Bar Harbor Statistical Genetics Workshop →Your Tasks
- 11:35, 22 July 2010 diff hist +284 Bar Harbor Statistical Genetics Workshop →Questions to Consider
- 11:31, 22 July 2010 diff hist +973 Bar Harbor Statistical Genetics Workshop →Plotting Regional Association Results
- 11:18, 22 July 2010 diff hist +829 Bar Harbor Statistical Genetics Workshop →Plotting Regional Association Results
- 09:24, 22 July 2010 diff hist +119 Bar Harbor Statistical Genetics Workshop →Plotting Regional Association Results
- 09:23, 22 July 2010 diff hist -2 Bar Harbor Statistical Genetics Workshop →Glusose Data Set
- 09:23, 22 July 2010 diff hist -15 Bar Harbor Statistical Genetics Workshop →Summary
- 09:23, 22 July 2010 diff hist 0 Bar Harbor Statistical Genetics Workshop →Example Data Set
- 09:22, 22 July 2010 diff hist +318 Bar Harbor Statistical Genetics Workshop →Generating a Q-Q Plot
- 09:19, 22 July 2010 diff hist +1,055 Bar Harbor Statistical Genetics Workshop →Example Data Set
- 09:16, 22 July 2010 diff hist +151 Bar Harbor Statistical Genetics Workshop →Generating a Q-Q Plot
- 09:15, 22 July 2010 diff hist +497 Bar Harbor Statistical Genetics Workshop →Generating a Q-Q Plot
- 09:12, 22 July 2010 diff hist +6 Bar Harbor Statistical Genetics Workshop
- 09:11, 22 July 2010 diff hist +970 Bar Harbor Statistical Genetics Workshop →Example Data Set
- 09:10, 22 July 2010 diff hist +60 N File:QQ-plot-problem.png QQ plot for a problematic study; from McCarthy et al (2008). current
- 09:09, 22 July 2010 diff hist +55 N File:QQ-plot-ideal.png QQ plot for an ideal study; from McCarthy et al (2008). current
- 09:09, 22 July 2010 diff hist +53 N File:QQ-plot-null.png QQ plot for a null study; from McCarthy et al (2008). current
- 08:57, 22 July 2010 diff hist 0 Bar Harbor Statistical Genetics Workshop →Example Data Set
- 08:57, 22 July 2010 diff hist +1,083 Bar Harbor Statistical Genetics Workshop →Summary
- 08:46, 22 July 2010 diff hist +44 N Short Workshops Created page with 'Bar Harbor Statistical Genetics Workshop'
- 08:45, 22 July 2010 diff hist +6 MediaWiki:Sidebar
- 08:45, 22 July 2010 diff hist +26 MediaWiki:Sidebar
- 08:43, 22 July 2010 diff hist +237 N Bar Harbor Statistical Genetics Workshop Created page with '== Summary == This workshop was prepared for the 51st Mammalian Genetics Short Course, at the Jackson Laboratory in Bar Harbor. It illustrates several simple analyses of genetic…'
- 17:28, 20 July 2010 diff hist +11 Biostatistics 666: Main Page →Problem Set Solutions
- 20:24, 15 July 2010 diff hist +255 Introduction to new students →Resources
- 12:58, 12 July 2010 diff hist +222 VcfCodingSnps
- 12:57, 12 July 2010 diff hist -501 m VcfCodingSnps Reverted edits by Freeseek (Talk) to last revision by Liyanmin
- 23:53, 27 June 2010 diff hist 0 Abecasis Lab →Former Doctoral Students
- 04:32, 22 June 2010 diff hist +235 N MERLIN format Created page with 'Files in '''MERLIN format''' describe genotypes and phenotypes for a set of individuals, as well as relationships between these individuals. The format is described at http://ww…' current
- 04:30, 22 June 2010 diff hist -1,288 BamGenotypeCheck
- 11:02, 17 June 2010 diff hist +933 Power Calculations: Quantitative Traits →A Simple Genetic Association Study current
- 10:55, 17 June 2010 diff hist +502 Power Calculations: Quantitative Traits →A Simple Genetic Association Study
- 10:50, 17 June 2010 diff hist -3 Power Calculations: Quantitative Traits →A Simple Genetic Association Study
- 10:49, 17 June 2010 diff hist +1,267 N Power Calculations: Quantitative Traits Created page with 'Calculating power for simple study designs is one of the most common tasks faced by a Biostatistician. However, for most of them, it barely makes the list of the top 1000 things …'
- 10:23, 16 June 2010 diff hist -7 GlfMultiples →Download current
- 01:30, 15 June 2010 diff hist +513 RelativeFinder →How It Works
- 01:27, 15 June 2010 diff hist 0 RelativeFinder →Download
- 01:26, 15 June 2010 diff hist +758 GlfMultiples →VCF Output
- 01:22, 15 June 2010 diff hist 0 GlfMultiples →Download
- 12:36, 9 June 2010 diff hist +18 N Mach moved Mach to MaCH current
- 12:36, 9 June 2010 diff hist 0 m MaCH moved Mach to MaCH
- 11:54, 9 June 2010 diff hist +135 METAL FAQ current
- 10:39, 4 June 2010 diff hist +115 MaCH: Input Files
- 10:38, 4 June 2010 diff hist -6 MaCH
- 10:38, 4 June 2010 diff hist -3,481 m MaCH
- 10:36, 4 June 2010 diff hist +208 MaCH: Input Files →Optional Phased Haplotypes
- 10:34, 4 June 2010 diff hist +346 MaCH: Input Files
- 10:32, 4 June 2010 diff hist +340 MaCH: Input Files →Observed Genotypes
- 10:31, 4 June 2010 diff hist +17 MaCH: Input Files →Optional Phased Haplotypes
- 10:25, 4 June 2010 diff hist +25 MaCH: Input Files →Observed Genotypes
- 10:24, 4 June 2010 diff hist +210 MaCH: Pedigree with Integer Allele Codes current
- 10:22, 4 June 2010 diff hist +439 N MaCH: Pedigree with Integer Allele Codes Created page with 'For compatibility with older applications that only accept integer allele codes in pedigree files, MaCH can accept pedigree files that encode bases A, C, G, T as 1, 2, 3, 4. Here…'
- 10:21, 4 June 2010 diff hist +1 MaCH: Input Files →Observed Genotypes
- 10:21, 4 June 2010 diff hist +6,394 N MaCH: Input Files Created page with 'MACH input files include information on experimental genotypes for a set of individuals and, optionally, on a set of known haplotypes. MACH can use these to estimate haplotypes f…'
- 07:52, 4 June 2010 diff hist -2 MaCH: 1000 Genomes Imputation Cookbook →Selecting a Subset of Samples
- 07:52, 4 June 2010 diff hist +1 MaCH: 1000 Genomes Imputation Cookbook →Selecting a Subset of Samples
- 07:17, 4 June 2010 diff hist +316 MaCH: 1000 Genomes Imputation Cookbook →Imputation
- 07:13, 4 June 2010 diff hist +900 MaCH: 1000 Genomes Imputation Cookbook →Selecting a Subset of Samples
- 07:08, 4 June 2010 diff hist +2,224 MaCH: 1000 Genomes Imputation Cookbook →Estimating Model Parameters
- 06:50, 4 June 2010 diff hist +548 MaCH: 1000 Genomes Imputation Cookbook →Estimating Model Parameters
- 06:47, 4 June 2010 diff hist +18 MaCH: 1000 Genomes Imputation Cookbook →Reference Haplotypes
- 06:45, 4 June 2010 diff hist -2 MaCH: 1000 Genomes Imputation Cookbook →Reference Haplotypes
- 06:45, 4 June 2010 diff hist +1,185 N MaCH: 1000 Genomes Imputation Cookbook Created page with 'This page documents how to impute 1000 Genome SNPs using MaCH. == Getting Started == === Your Own Data === To get started, you will need to store your data in Merlin form…'
- 06:31, 4 June 2010 diff hist +102 MaCH
- 06:29, 4 June 2010 diff hist -7,695 MaCH →FAQ
- 06:28, 4 June 2010 diff hist +7,638 N MaCH FAQ Created page with '== Why and how to perform a 2-step imputation? == When one has a large number of individuals (>1000), we recommend a 2-step imputation to speed up. <br> …'
- 06:22, 4 June 2010 diff hist -7 MaCH →FAQ
- 06:21, 4 June 2010 diff hist +368 MaCH
- 06:02, 4 June 2010 diff hist -112 MaCH →Examples
- 06:01, 4 June 2010 diff hist -148 MaCH →Options
- 06:01, 4 June 2010 diff hist -28 MaCH →Parameter files
- 06:00, 4 June 2010 diff hist +54 MaCH →Input Files
- 05:23, 4 June 2010 diff hist +103 PedScript →SET = current
- 05:22, 4 June 2010 diff hist +1 PedScript →= HELP
- 05:22, 4 June 2010 diff hist +2,195 PedScript
- 05:07, 4 June 2010 diff hist 0 PedScript →Download
- 05:07, 4 June 2010 diff hist +178 N PedScript Created page with 'Category: Software == Download == Source tarball for pedscript is available from [http://www.sph.umich.edu/csg/abecasis/downloads/generic-pedscript-2010-06-03.tar.gz here].'
- 04:37, 4 June 2010 diff hist -7 MaCH →Can I used unphased reference?
- 04:36, 4 June 2010 diff hist +10 MaCH →More questions?
- 04:35, 4 June 2010 diff hist -42 MaCH →How long does imputation take?
- 03:36, 4 June 2010 diff hist +1 GlfMerge current
- 03:36, 4 June 2010 diff hist +126 N GlfMerge Created page with ''''glfMerge''' merges genotype likelihoods stored in multiple GLFfiles. It is useful when combining data across platforms.'
- 03:34, 4 June 2010 diff hist +3 GLF →Generating GLF Files for a Specific Region
- 13:29, 2 June 2010 diff hist -1 BamUtil
- 13:28, 2 June 2010 diff hist +17 N C++ Executable: bam moved C++ Executable: bam to Bam: End users won't care that it is a c++ executable. current
- 13:28, 2 June 2010 diff hist 0 m BamUtil moved C++ Executable: bam to Bam: End users won't care that it is a c++ executable.
- 13:26, 2 June 2010 diff hist -1 FastQValidator
- 13:26, 2 June 2010 diff hist +33 N Talk:C++ Executable: fastQValidator moved Talk:C++ Executable: fastQValidator to Talk:FastQValidator: end users won't care whether this is a C++ or Pascal executable current
- 13:26, 2 June 2010 diff hist 0 m Talk:FastQValidator moved Talk:C++ Executable: fastQValidator to Talk:FastQValidator: end users won't care whether this is a C++ or Pascal executable current
- 13:26, 2 June 2010 diff hist +28 N C++ Executable: fastQValidator moved C++ Executable: fastQValidator to FastQValidator: end users won't care whether this is a C++ or Pascal executable current
- 13:26, 2 June 2010 diff hist 0 m FastQValidator moved C++ Executable: fastQValidator to FastQValidator: end users won't care whether this is a C++ or Pascal executable
- 13:22, 2 June 2010 diff hist 0 New Fugue →Download
- 00:51, 1 June 2010 diff hist +2 SAM
- 00:50, 1 June 2010 diff hist +17 N SAM Format Redirected page to SAM current
- 00:50, 1 June 2010 diff hist +104 SAM
- 00:47, 1 June 2010 diff hist +17 N BAM Format moved BAM Format to BAM current
- 00:47, 1 June 2010 diff hist 0 m BAM moved BAM Format to BAM
- 00:45, 1 June 2010 diff hist 0 GLF →Generating GLF Files for a Specific Region
- 00:45, 1 June 2010 diff hist +482 GLF →Generating GLF Files
- 20:45, 30 May 2010 diff hist -4 VcfCodingSnps
- 20:44, 30 May 2010 diff hist +650 N Indel Created page with 'An ''indel'' is a short polymorphism that corresponds to the addition or removal of a small number of bases in a DNA sequence. Indels are quite abundant, although not quite as ab…' current
- 20:40, 30 May 2010 diff hist -2 Gzip →References
- 20:40, 30 May 2010 diff hist +399 N Gzip Created page with '''Gzip'' is a widely used file compression utility, developed by Mark Adler and Jean Loup Gailly. The source code and algorithm for the gzip are well documented and widely availa…'
- 20:36, 30 May 2010 diff hist +176 N Biostatistics 666: Whole Genome Sequencing Created page with '== Objective == Introduce the statistical and computational challenges of contemporary whole genome sequencing. == Lecture Notes == Slides in PDF Format'
- 00:46, 27 May 2010 diff hist +4 Metal Redirected page to METAL current
- 00:45, 27 May 2010 diff hist +15 N Metal Created page with '#REDIRECT METAL'
- 12:08, 26 May 2010 diff hist -38 Meta Analysis of SNPxEnvironment Interaction →Implementation
- 10:37, 26 May 2010 diff hist +1 Biostatistics 666: Linkage Tests for Pairs of Individuals current
- 16:16, 25 May 2010 diff hist 0 GlfMultiples →Download
- 13:35, 25 May 2010 diff hist +250 GlfMultiples →Command Line Options
- 11:06, 25 May 2010 diff hist +17 LocusZoom Standalone →Batch mode
- 11:05, 25 May 2010 diff hist +74 New Fugue →Linkage Disequilibrium File Options
- 11:04, 25 May 2010 diff hist -12 New Fugue →Command Line Options
- 11:04, 25 May 2010 diff hist +1,383 New Fugue
- 10:54, 25 May 2010 diff hist -26 New Fugue →Download
- 16:17, 24 May 2010 diff hist -56 MaCH →How do I get imputation quality estimates?
- 16:16, 24 May 2010 diff hist -3 MaCH →Does --mle overwrite input genotypes?
- 16:16, 24 May 2010 diff hist +28 MaCH →Does --mle overwrite fed-in genotypes?
- 16:14, 24 May 2010 diff hist -3 MaCH →Why and how to perform a 2-step imputation?
- 16:14, 24 May 2010 diff hist -3 MaCH →How is AL1 defined? Which allele dosage is .dose/.mldose counting?
- 16:13, 24 May 2010 diff hist -3 MaCH →How do I get reference files for an region of interest?
- 16:13, 24 May 2010 diff hist -2 MaCH →How do I get reference files for an region of interest?
- 16:12, 24 May 2010 diff hist -6 MaCH →How do I get reference files for an region of interest?
- 16:12, 24 May 2010 diff hist -110 MaCH →How do I get reference files for an region of interest?
- 16:10, 24 May 2010 diff hist -7 MaCH →Shall I apply QC before or after imputation? If so, how?
- 16:10, 24 May 2010 diff hist -9 MaCH →Shall I apply QC before or after imputation? If so, how?
- 16:10, 24 May 2010 diff hist +40 MaCH →Do I have to sort the pedigree file by physical positions?
- 16:09, 24 May 2010 diff hist 0 MaCH →What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)?
- 16:08, 24 May 2010 diff hist -536 MaCH →Can I used unphased reference?
- 16:01, 24 May 2010 diff hist +531 MaCH →How is AL1 defined? Which allele dosage is .dose/.mldose counting?
- 15:53, 24 May 2010 diff hist -20 MaCH →How is AL1 defined? Which allele dosage is .dose/.mldose counting?