User contributions
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Jump to navigationJump to search- 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?
- 07:15, 22 May 2010 diff hist 0 GlfMultiples →Download
- 13:07, 21 May 2010 diff hist +7 Generic Exome Analysis Plan →Read Mapping current
- 02:52, 21 May 2010 diff hist 0 GlfMultiples →Download
- 05:42, 20 May 2010 diff hist -1 GlfMultiples →VCF Output
- 05:42, 20 May 2010 diff hist -8 GlfMultiples →VCF Output
- 05:42, 20 May 2010 diff hist +413 GlfMultiples →Filtering According to Depth and Map Quality
- 05:38, 20 May 2010 diff hist +9 GlfMultiples →X Chromosome Variant Calling
- 05:38, 20 May 2010 diff hist +130 GlfMultiples →Model for Variant Calling
- 00:16, 20 May 2010 diff hist +22 Merlin current
- 00:16, 20 May 2010 diff hist 0 RelativeFinder →Alternative Relationships
- 00:15, 20 May 2010 diff hist +24 RelativeFinder →Alternative Relationships
- 00:14, 20 May 2010 diff hist +8 RelativeFinder →Alternative Relationships
- 00:14, 20 May 2010 diff hist +4,960 N RelativeFinder Created page with 'Category:Software '''relativeFinder''' is a program for checking relationships between pairs of individuals. There are many excellent programs that carry out similar tasks. S…'
- 22:11, 18 May 2010 diff hist +24 N ExomePicks Program moved ExomePicks Program to ExomePicks: Make naming consistent with that of other software utilities current
- 22:11, 18 May 2010 diff hist 0 m ExomePicks moved ExomePicks Program to ExomePicks: Make naming consistent with that of other software utilities
- 22:10, 18 May 2010 diff hist -1 MaCH
- 22:09, 18 May 2010 diff hist +14 MaCH
- 09:01, 17 May 2010 diff hist +273 METAL Documentation →Selecting an Analysis Scheme
- 08:57, 17 May 2010 diff hist +23 N LocusZoom Documentation moved LocusZoom Documentation to LocusZoom over redirect current
- 08:57, 17 May 2010 diff hist 0 m LocusZoom moved LocusZoom Documentation to LocusZoom over redirect
- 08:56, 17 May 2010 diff hist +19 N METAL Program moved METAL Program to METAL current
- 08:56, 17 May 2010 diff hist 0 m METAL moved METAL Program to METAL
- 13:54, 11 May 2010 diff hist +24 New Fugue
- 09:16, 11 May 2010 diff hist +702 N New Fugue Created page with '''New Fugue'' is a program for estimation of haplotype frequencies and linkage disequilibrium coefficients in family data. The current implementation uses the methods described b…'
- 01:48, 8 May 2010 diff hist +62 Abecasis Lab →Research Fellows
- 01:47, 8 May 2010 diff hist +24 Abecasis Lab →Staff
- 01:46, 8 May 2010 diff hist +1 Abecasis Lab →Research Fellows
- 01:46, 8 May 2010 diff hist +22 Abecasis Lab →Research Fellows
- 19:26, 7 May 2010 diff hist +2,205 TinySimulator →Command Line Options current
- 19:15, 7 May 2010 diff hist +22 TinySimulator
- 19:15, 7 May 2010 diff hist +22 GlfTrio
- 19:14, 7 May 2010 diff hist +5 GlfMultiples →Basic Usage Example
- 19:14, 7 May 2010 diff hist +22 GlfMultiples
- 19:13, 7 May 2010 diff hist +22 ExomePicks
- 19:13, 7 May 2010 diff hist +59 ExomePicks
- 14:29, 5 May 2010 diff hist +190 Generic Exome Analysis Plan →Variant Filters
- 11:14, 2 May 2010 diff hist +730 N TinySimulator Created page with 'The '''tinySimulator''' is a small and (somewhat) memory efficient forward simulator. It simulates DNA sequences over time, allowing for the possibility of mutation, recombinatio…'
- 10:25, 29 April 2010 diff hist -10 Verifying Sample Identities - Implementation →Mathematical Details current
- 13:22, 23 April 2010 diff hist +211 SardiNIA →Key References
- 13:22, 23 April 2010 diff hist +1,006 SardiNIA →Project Leaders
- 11:51, 21 April 2010 diff hist -1 Generic Exome Analysis Plan →Read Mapping
- 11:50, 21 April 2010 diff hist +27 Generic Exome Analysis Plan →Read Mapping
- 08:02, 21 April 2010 diff hist +3 Generic Exome Analysis Plan →Variant Filters
- 07:14, 21 April 2010 diff hist +415 Generic Exome Analysis Plan →Read Mapping
- 00:30, 21 April 2010 diff hist +228 Generic Exome Analysis Plan →Read Mapping
- 00:28, 21 April 2010 diff hist +112 Generic Exome Analysis Plan
- 00:28, 21 April 2010 diff hist +199 Generic Exome Analysis Plan →Generate Variant Calls
- 00:27, 21 April 2010 diff hist +1,272 Generic Exome Analysis Plan →Special Considerations for Admixed Samples
- 00:13, 21 April 2010 diff hist 0 Kyoto Encyclopedia of Genes and Genomes →Website current
- 00:13, 21 April 2010 diff hist +13 Kyoto Encyclopedia of Genes and Genomes →Website
- 00:12, 21 April 2010 diff hist +294 Nm Kyoto Encyclopedia of Genes and Genomes Created page with 'The Kyoto Encyclopedia of Genes and Genomes ('''KEGG''') is a popular, curated resource summarizing information about gene function in a manner that allows genes with similar fun…'
- 00:09, 21 April 2010 diff hist -1 Generic Exome Analysis Plan →Visualize Results =
- 00:08, 21 April 2010 diff hist -1 Generic Exome Analysis Plan →More Q-Q Plots =
- 00:08, 21 April 2010 diff hist +2,638 Generic Exome Analysis Plan
- 23:55, 20 April 2010 diff hist +687 Generic Exome Analysis Plan →Special Considerations for Admixed Samples
- 23:51, 20 April 2010 diff hist +123 Generic Exome Analysis Plan →Generate Variant Calls
- 23:49, 20 April 2010 diff hist -2 Generic Exome Analysis Plan →Prior to Mapping
- 23:48, 20 April 2010 diff hist -2 Generic Exome Analysis Plan →Read Mapping and Variant Calling
- 23:48, 20 April 2010 diff hist +3,032 Generic Exome Analysis Plan →Read Mapping
- 23:34, 20 April 2010 diff hist +1,899 N Generic Exome Analysis Plan Created page with 'This page outlines a generic plan for analysis of a whole exome sequencing project. The idea is that the points listed here might serve as a starting point for discussion of the …'
- 15:22, 20 April 2010 diff hist -7 Verifying Sample Identities - Implementation →Mathematical Details
- 10:06, 20 April 2010 diff hist 0 File:666.21.pdf uploaded a new version of "File:666.21.pdf" current
- 08:39, 20 April 2010 diff hist +75 Biostatistics 666: Main Page →Class Notes
- 08:38, 20 April 2010 diff hist 0 N File:666.21.pdf
- 13:44, 15 April 2010 diff hist +726 ExomePicks →Acknowledgements
- 10:13, 15 April 2010 diff hist 0 Abecasis Lab →Former Doctoral Students
- 10:12, 15 April 2010 diff hist +42 N Goncalo Abecasis Created page with '300px|center'
- 10:12, 15 April 2010 diff hist -44 Main Page →Abecasis Group Meeting
- 10:11, 15 April 2010 diff hist -1 FastQValidator →Required Parameters
- 10:10, 15 April 2010 diff hist -2 FastQValidator →Examples
- 09:42, 15 April 2010 diff hist -165 LocusZoom →Commonly Used LocusZoom Options
- 09:38, 15 April 2010 diff hist +1 LocusZoom →Commonly Used LocusZoom Options
- 09:38, 15 April 2010 diff hist +3,798 LocusZoom →Generate single plots using our publicly-available lipids GWAS data
- 09:25, 15 April 2010 diff hist -5,026 LocusZoom →Generate single plots using our publicly-available lipids GWAS data
- 09:23, 15 April 2010 diff hist +1,051 LocusZoom →Uploading Your Association Study Results
- 09:16, 15 April 2010 diff hist +309 LocusZoom →Uploading Your Association Study Results
- 09:13, 15 April 2010 diff hist -8 LocusZoom →Generating a Hit Spec File
- 09:12, 15 April 2010 diff hist +36 LocusZoom →Generating a Hit Spec File
- 09:12, 15 April 2010 diff hist +10 LocusZoom →Generating a Hit Spec File
- 09:12, 15 April 2010 diff hist -10 LocusZoom →Generating a Hit Spec File
- 09:11, 15 April 2010 diff hist +12 LocusZoom →Generating a Hit Spec File
- 09:11, 15 April 2010 diff hist -12 LocusZoom →Generating a Hit Spec File
- 09:10, 15 April 2010 diff hist +875 LocusZoom →Generating a Hit Spec File
- 00:35, 14 April 2010 diff hist +19 LocusZoom →Generating a Hit Spec File
- 00:35, 14 April 2010 diff hist -6 LocusZoom →Generating a Hit Spec File
- 00:34, 14 April 2010 diff hist -536 LocusZoom →Uploading your own file and use the batch mode
- 00:31, 14 April 2010 diff hist +2 LocusZoom →Customizing the Display of Your Results
- 00:31, 14 April 2010 diff hist +2 LocusZoom →Upload your own meta-analysis file and generate single plots using a web-based form
- 00:20, 14 April 2010 diff hist -16 LocusZoom →LocusZoom
- 00:20, 14 April 2010 diff hist +1 LocusZoom
- 00:19, 14 April 2010 diff hist +1,062 LocusZoom
- 00:09, 14 April 2010 diff hist 0 N File:LocusZoomSmall.png current
- 00:04, 14 April 2010 diff hist -20 LocusZoom →Generate single plots using our publicly-available lipids GWAS data
- 00:02, 14 April 2010 diff hist +12 LocusZoom →Generate single plots using our publicly-available lipids GWAS data
- 23:58, 13 April 2010 diff hist +22 LocusZoom
- 23:57, 13 April 2010 diff hist +22 METAL
- 23:57, 13 April 2010 diff hist -1 GlfSingle
- 23:57, 13 April 2010 diff hist +94 N Category:Software Created page with 'This page provides a convenient index to all the '''software''' tools documented in this wiki.' current
- 23:53, 13 April 2010 diff hist +92 GlfSingle →Command Line Options
- 17:27, 12 April 2010 diff hist +102 ExomePicks →Acknowledgements
- 03:55, 12 April 2010 diff hist +159 ExomePicks
- 03:54, 12 April 2010 diff hist 0 ExomePicks →Download
- 00:55, 8 April 2010 diff hist +107 Biostatistics 666: Variance Component Analyses
- 00:54, 8 April 2010 diff hist 0 File:666.19.pdf uploaded a new version of "File:666.19.pdf" current
- 00:54, 8 April 2010 diff hist 0 N File:666.20.pdf
- 23:15, 7 April 2010 diff hist +255 N Biostatistics 666: Variance Component Analyses Created page with '== Lecture Notes == Slides in PDF Format == References == Amos (1994) ''Am J Hum Genet'' '''54''':535-543 Hopper and Matthews (1982) ''Ann Hum Genet'' ''…'
- 23:14, 7 April 2010 diff hist +79 Biostatistics 666: Main Page →Class Notes
- 23:13, 7 April 2010 diff hist 0 Biostatistics 666: Applications of the Lander-Green Algorithm →References current
- 23:13, 7 April 2010 diff hist +143 Biostatistics 666: Applications of the Lander-Green Algorithm →References
- 03:55, 6 April 2010 diff hist 0 File:666.19.pdf uploaded a new version of "File:666.19.pdf"
- 02:57, 6 April 2010 diff hist +479 N Biostatistics 666: Applications of the Lander-Green Algorithm Created page with '== Outline == This lecture outlines three useful applications of the inheritance vector concept that was first introduced in the Lander-Green algorithm. The applications are the…'
- 02:43, 6 April 2010 diff hist +95 N File:666.19.pdf Non-parametric linkage analysis, parametric linkage analysis, information content calculations.
- 02:42, 6 April 2010 diff hist +94 Biostatistics 666: Main Page →Class Notes
- 00:51, 6 April 2010 diff hist +410 METAL
- 00:47, 6 April 2010 diff hist +16 METAL →Option Specific Pages
- 00:47, 6 April 2010 diff hist +350 METAL →Useful Wiki Pages
- 00:43, 6 April 2010 diff hist +125 METAL Command Reference →General Analysis Control
- 00:41, 6 April 2010 diff hist +39 METAL Command Reference →Describing Input Files
- 00:39, 6 April 2010 diff hist +463 N METAL EFFECTLABEL Created page with 'Effect sizes can be log transformed on the fly. This is convenient when meta-analyzing odds ratios. In this case, two studies have the same direction of effect if their log(odds …' current
- 00:39, 6 April 2010 diff hist +820 N METAL SOURCE Created page with 'The '''SOURCE''' command allows one script to include another script. This can be convenient when you want to try multiple analyses that include similar filesets. For example, if…' current
- 00:37, 6 April 2010 diff hist +32 METAL Command Reference →General Analysis Control
- 00:36, 6 April 2010 diff hist +691 N METAL VERBOSE Created page with 'The '''VERBOSE''' option is enabled with the <code>VERBOSE ON</code> command. When this option is enabled METAL will print details of each analyzed SNP for each input file. Unles…' current
- 00:34, 6 April 2010 diff hist +79 METAL Command Reference →General Analysis Control
- 00:33, 6 April 2010 diff hist +75 METAL Command Reference →Genomic Control Correction of Input Statistics
- 00:33, 6 April 2010 diff hist +77 METAL Command Reference →User Defined Variables
- 00:32, 6 April 2010 diff hist +2 METAL ADDFILTER current
- 00:32, 6 April 2010 diff hist +72 METAL Command Reference →Filtering Input Files
- 00:31, 6 April 2010 diff hist +2 METAL Command Reference →Describing Input Files
- 00:31, 6 April 2010 diff hist +87 METAL Command Reference →Describing Input Files
- 00:30, 6 April 2010 diff hist +520 N METAL ADDFILTER Created page with 'The '''ADDFILTER''' command allows filters based on simple comparison operators to be applied to input files. For example, the following commands would filter each input file acc…'
- 00:27, 6 April 2010 diff hist +662 N METAL GENOMICCONTROL Created page with 'The '''GENOMICCONTROL''' setting defaults to off, which means that no correction is applied to input studies. Setting <code>GENOMICCONTROL ON</code> requests that METAL should a…'
- 00:24, 6 April 2010 diff hist +29 METAL CUSTOMVARIABLE current
- 00:24, 6 April 2010 diff hist +31 METAL CUSTOMVARIABLE
- 00:23, 6 April 2010 diff hist +774 N METAL CUSTOMVARIABLE Created page with 'METAL '''CustomVariables''' are user specified columns whose contents are tracked across multiple files. New variables are created with the CUSTOMVARIABLE command. For example,…'
- 00:22, 6 April 2010 diff hist +249 N METAL LOGPVALUE Created page with 'When the '''LOGPVALUE''' option is set to ON, Metal now reports log<sub>10</sub>(p-value) instead of the raw p-value for meta-analysis and heterogeneity test results. This makes …' current
- 00:21, 6 April 2010 diff hist +218 N METAL COLUMNCOUNTING Created page with 'When the '''COLUMNCOUNTING''' option is set to STRICT (the default is LENIENT) METAL requires every line in an input file to have the exact same number of columns. This stricter …' current
- 00:13, 6 April 2010 diff hist +60 METAL Documentation →Useful Wiki Pages
- 13:37, 5 April 2010 diff hist -2 METAL FAQ
- 13:37, 5 April 2010 diff hist 0 METAL FAQ
- 13:37, 5 April 2010 diff hist +198 METAL FAQ
- 13:11, 5 April 2010 diff hist +31 METAL Quick Start →Extracting Study by Study Results For Individual SNPs current
- 13:11, 5 April 2010 diff hist +1,118 METAL Quick Start →Meta-Analysis Results
- 13:05, 5 April 2010 diff hist -6 METAL Quick Start →Meta-Analysis Results
- 13:04, 5 April 2010 diff hist +130 METAL Quick Start →Meta-Analysis Results
- 13:03, 5 April 2010 diff hist +169 METAL Quick Start →Meta-Analysis Results
- 13:01, 5 April 2010 diff hist -18 METAL Quick Start
- 13:00, 5 April 2010 diff hist +2,196 METAL Quick Start →Meta-Analysis Results
- 12:46, 5 April 2010 diff hist +31 METAL Quick Start →Describing the SardiNIA Input Files
- 12:46, 5 April 2010 diff hist +2 METAL Quick Start →Describing the SardiNIA Input Files
- 12:46, 5 April 2010 diff hist +1,407 METAL Quick Start →Describing the SardiNIA Input Files
- 12:41, 5 April 2010 diff hist +604 METAL Quick Start →Describing the FUSION Input Files
- 12:40, 5 April 2010 diff hist +604 METAL Quick Start →Describing the DGI Input Files
- 12:30, 5 April 2010 diff hist +260 METAL Quick Start →Acknowledgements
- 12:28, 5 April 2010 diff hist +16 METAL Quick Start →Extracting Study by Study Results For Individual SNPs
- 12:27, 5 April 2010 diff hist +4,005 METAL Quick Start →Describing the SardiNIA Input Files
- 12:09, 5 April 2010 diff hist +12 METAL Quick Start →Describing the FUSION Input Files
- 12:08, 5 April 2010 diff hist +107 N Gzip File Created page with 'A file compressed with the venerable [http://www.gzip.org gzip] program by Mark Adler and Jean-loup Gailly.'
- 12:05, 5 April 2010 diff hist +8 METAL Quick Start →Describing the FUSION Input Files
- 12:04, 5 April 2010 diff hist +1,216 METAL Quick Start →Describing the FUSION Input Files
- 11:59, 5 April 2010 diff hist +187 METAL Quick Start →Describing the DGI Input Files
- 11:58, 5 April 2010 diff hist +204 METAL Quick Start →Describing the DGI Input Files
- 11:57, 5 April 2010 diff hist +23 METAL →Useful Wiki Pages
- 11:56, 5 April 2010 diff hist 0 METAL →Useful Wiki Pages
- 11:56, 5 April 2010 diff hist +63 METAL →Useful Wiki Pages
- 11:55, 5 April 2010 diff hist -1 Stouffer Method for Meta-Analysis →Original Reference current
- 11:55, 5 April 2010 diff hist +1,269 N Stouffer Method for Meta-Analysis Created page with 'This is a method for meta-analysis of data across studies that requires only a p-value, sample size and estimated direction of effect for each study. We rediscovered it when impl…'
- 11:49, 5 April 2010 diff hist 0 METAL Quick Start →Describing the DGI Input Files
- 11:47, 5 April 2010 diff hist +16 METAL Quick Start →Describing the DGI Input Files
- 11:47, 5 April 2010 diff hist +6 METAL Quick Start →Describing the DGI Input Files
- 11:46, 5 April 2010 diff hist +1,759 METAL Quick Start →The METAL Script
- 01:32, 2 April 2010 diff hist +21 Gene Ontology →External Link current
- 01:32, 2 April 2010 diff hist +1,205 N Gene Ontology Created page with ''''Gene Ontology''' is a structured annotation of genes that encodes information about their biological function. It is a useful aid when interpreting results of micro-array stud…'
- 00:52, 1 April 2010 diff hist +367 N Biostatistics 666: The Lander-Green Algorithm Created page with '== Objective == This lecture introduces the Lander-Green algorithm as an extension of the algorithms for sibling pair analysis that we have described earlier in the course. == …' current
- 00:50, 1 April 2010 diff hist +38 N File:666.18.pdf Introduces the Lander-Green algorithm. current
- 00:49, 1 April 2010 diff hist +14 MediaWiki:Sidebar
- 00:49, 1 April 2010 diff hist +42 N Biostatistics 666 Redirected page to Biostatistics 666: Main Page current
- 00:47, 1 April 2010 diff hist +39 MediaWiki:Sidebar
- 00:35, 1 April 2010 diff hist 0 File:666.17.pdf uploaded a new version of "File:666.17.pdf"
- 00:34, 1 April 2010 diff hist +78 Biostatistics 666: Main Page →Class Notes
- 18:35, 30 March 2010 diff hist +130 C++ Class: SamFile
- 18:31, 30 March 2010 diff hist +126 C++ Class: SamFile
- 17:52, 30 March 2010 diff hist +8,000 N C++ Class: SamFile Created page with '== Reading/Writing SAM/BAM Files In Your Program == === Reading/Writing Standard SAM/BAM Files === The '''SamFile''' class allows a user to easily read/write a SAM/BAM file. The…'
- 17:18, 30 March 2010 diff hist +21 LibStatGen: FASTQ
- 16:09, 30 March 2010 diff hist -2 METAL Quick Start →Running METAL
- 16:08, 30 March 2010 diff hist -32 METAL Quick Start →Running METAL
- 11:39, 30 March 2010 diff hist +7 GWAS current
- 11:39, 30 March 2010 diff hist +357 GWAS
- 11:37, 30 March 2010 diff hist +4 METAL Documentation →Genomic Control Correction
- 08:42, 30 March 2010 diff hist 0 Biostatistics 666: Main Page →Scheduling
- 07:33, 30 March 2010 diff hist +32 METAL Quick Start →Running METAL
- 07:32, 30 March 2010 diff hist -6 METAL Quick Start →Running METAL
- 07:31, 30 March 2010 diff hist +441 METAL Quick Start →Running METAL
- 07:28, 30 March 2010 diff hist +48 METAL Quick Start →Running METAL
- 07:27, 30 March 2010 diff hist +685 METAL Quick Start →Running METAL
- 07:22, 30 March 2010 diff hist +787 METAL Quick Start →The METAL Script
- 07:14, 30 March 2010 diff hist +1,825 N METAL Glucose Example Script Created page with '<source lang="text"> # This file includes a series of comments. Each comment is marked # by a # character as the first character in the line. # # This is a comment! # Meta-anal…' current
- 07:05, 30 March 2010 diff hist +271 METAL Quick Start
- 07:02, 30 March 2010 diff hist +481 METAL Quick Start →Input Files
- 06:59, 30 March 2010 diff hist +39 METAL Quick Start →Input Files
- 06:58, 30 March 2010 diff hist +906 METAL Quick Start
- 06:43, 30 March 2010 diff hist +294 METAL Quick Start →The Glucose Data
- 06:40, 30 March 2010 diff hist +1 METAL Quick Start →Learning by Example
- 06:40, 30 March 2010 diff hist +841 N METAL Quick Start Created page with '== Learning by Example == Many people find that it easiest to learn by example. So, if reading through our ''extensive'' [METAL Documentation|documentation] is not for you, you …'
- 06:13, 30 March 2010 diff hist +218 METAL Documentation
- 06:08, 30 March 2010 diff hist +33 N Metal Documentation moved Metal Documentation to METAL Documentation current
- 06:08, 30 March 2010 diff hist 0 m METAL Documentation moved Metal Documentation to METAL Documentation
- 05:59, 30 March 2010 diff hist -3 Biostatistics 666: Relationship Checking →Recommended Reading current
- 05:59, 30 March 2010 diff hist +529 N Biostatistics 666: Relationship Checking Created page with '== Objective == Introduce the idea that checking genetic relationships is a critical part of genetic studies. Discuss different approaches for checking genetic relationships and…'
- 05:56, 30 March 2010 diff hist +131 N File:666.17.pdf Describes approaches for multipoint analysis in different relative pairs. Describes approaches for checking genetic relationships.
- 05:55, 30 March 2010 diff hist +73 Biostatistics 666: Main Page →Class Notes
- 11:13, 25 March 2010 diff hist +2 METAL Documentation →Advanced Analysis Options
- 11:13, 25 March 2010 diff hist -1 METAL Documentation →Advanced Analysis Options
- 11:11, 25 March 2010 diff hist +11 METAL Documentation →Usage instructions
- 11:10, 25 March 2010 diff hist -29 METAL Documentation →Analyze Heterogeneity
- 11:10, 25 March 2010 diff hist +8 METAL Documentation →Filtering
- 11:09, 25 March 2010 diff hist +223 METAL Documentation →Filtering
- 11:08, 25 March 2010 diff hist +33 METAL Documentation
- 11:06, 25 March 2010 diff hist +333 METAL Documentation →Performing the Final Analysis
- 11:05, 25 March 2010 diff hist -552 METAL Documentation →Filtering
- 11:04, 25 March 2010 diff hist +664 METAL Documentation →Input File Columns
- 11:01, 25 March 2010 diff hist -418 METAL Documentation →Verbose Mode
- 10:57, 25 March 2010 diff hist -2 METAL Documentation →Example: A METAL Meta-Analysis Script
- 10:57, 25 March 2010 diff hist +7 METAL Documentation →Example text file to run metal;
- 10:56, 25 March 2010 diff hist +6 METAL Documentation
- 10:55, 25 March 2010 diff hist -325 METAL Documentation
- 10:46, 25 March 2010 diff hist +514 METAL Documentation →Input Files
- 10:44, 25 March 2010 diff hist -361 METAL Documentation →Input File Recommendations
- 10:29, 25 March 2010 diff hist +1,511 METAL Documentation
- 03:17, 25 March 2010 diff hist +312 METAL Documentation
- 03:06, 25 March 2010 diff hist +97 METAL Documentation →Authors
- 03:04, 25 March 2010 diff hist +1,674 METAL Documentation →Usage instructions
- 02:42, 25 March 2010 diff hist +1,089 METAL Documentation
- 02:26, 25 March 2010 diff hist +37 N Metal Command Reference moved Metal Command Reference to METAL Command Reference current
- 02:26, 25 March 2010 diff hist 0 m METAL Command Reference moved Metal Command Reference to METAL Command Reference
- 02:26, 25 March 2010 diff hist +26 METAL →Useful Wiki Pages
- 02:25, 25 March 2010 diff hist +4 METAL →Useful Wiki Pages
- 02:23, 25 March 2010 diff hist +489 N METAL Created page with 'METAL is a program that facilitates the meta-analysis of genomewide association scans. == Useful Wiki Pages == There are a few pages in this Wiki that may be useful to METAL us…'
- 02:21, 25 March 2010 diff hist +2 METAL FAQ
- 02:20, 25 March 2010 diff hist -8 METAL FAQ
- 02:19, 25 March 2010 diff hist +24 METAL FAQ
- 02:18, 25 March 2010 diff hist +960 N METAL FAQ Created page with 'This is the Frequently Asked Questions page for the [METAL Program] ;# Metal checks whether the direction of effect is positive or negative when combining information across sam…'
- 13:01, 24 March 2010 diff hist +133 GlfSingle
- 12:24, 24 March 2010 diff hist -7 GlfSingle →Command Line Options
- 11:04, 24 March 2010 diff hist +67 Biostatistics 666: Main Page →Scheduling
- 11:01, 24 March 2010 diff hist +324 Biostatistics 666: Main Page
- 19:39, 23 March 2010 diff hist +165 FASTA current
- 19:37, 23 March 2010 diff hist -2 FASTA →Example
- 19:37, 23 March 2010 diff hist +680 N FASTA Created page with 'A simple text format for storing DNA sequences. A FASTA file can store one or more DNA sequences. Each record in a FASTA file begins with a > character (which must be the fir…'
- 19:33, 23 March 2010 diff hist +2 Biostatistics 666: Multipoint Analysis in Sibling Pairs →Slides current
- 19:33, 23 March 2010 diff hist +154 N Biostatistics 666: Multipoint Analysis in Sibling Pairs Created page with '== Outline == This lecture introduces the principles behind multipoint analysis of sibling pairs. == Slides == [Media:666.16.pdf|Slides in PDF Format]'
- 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 …'