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Jump to navigationJump to search- 02:51, 19 December 2009 diff hist +76 BAM
- 02:50, 19 December 2009 diff hist +237 N SAM Created page with 'The '''SAM Format''' is a text format for storing aligned reads. The current definition of the format is at http://samtools.sourceforge.net/SAM1.pdf BAM/SAM Specification. …'
- 02:48, 19 December 2009 diff hist +670 Mapping Quality Scores
- 11:53, 18 December 2009 diff hist +147 GLF →Tools That Use GLF Files
- 19:05, 17 December 2009 diff hist -5 CHARGE →Reference current
- 19:05, 17 December 2009 diff hist +88 CHARGE
- 18:40, 17 December 2009 diff hist +44 Main Page →Read Mapping
- 18:38, 17 December 2009 diff hist +172 Mapping Quality Scores
- 18:34, 17 December 2009 diff hist +743 N Mapping Quality Scores Created page with ''''Mapping Quality Scores''' quantify the probability that a read is misplaced. They were introduced by Heng Li and Richard Durbin in their paper describing MAQ and are usually r…'
- 15:00, 15 December 2009 diff hist +262 N CHARGE Created page with ''''CHARGE''' is a consortium of several population based cohorts. The acronym stands for Cohorts for Health and Aging Related Genetic Epidemiology. == Participating Cohorts == …'
- 14:46, 15 December 2009 diff hist +46 N GWAS Created page with ''''GWAS''' are genomewide association studies.'
- 15:55, 14 December 2009 diff hist -2 Main Page
- 14:38, 14 December 2009 diff hist +179 N BAM Created page with 'The '''BAM Format''' is a binary format for storing aligned reads. The current definition of the format is at http://samtools.sourceforge.net/SAM1.pdf BAM/SAM Specification…'
- 13:12, 14 December 2009 diff hist +117 N Talk:Examples of Read Mapping with Karma and BWA Created page with 'We need a much more informative title for this page. Also, it needs to linked (in some sensible way) to other pages.'
- 12:37, 14 December 2009 diff hist +1 Examples of Read Mapping with Karma and BWA
- 12:37, 14 December 2009 diff hist +13 Examples of Read Mapping with Karma and BWA
- 12:36, 14 December 2009 diff hist -2 Examples of Read Mapping with Karma and BWA
- 12:36, 14 December 2009 diff hist -6 Examples of Read Mapping with Karma and BWA
- 12:35, 14 December 2009 diff hist +4 SardiNIA →Key References
- 12:35, 14 December 2009 diff hist +142 SardiNIA
- 12:34, 14 December 2009 diff hist +199 SardiNIA
- 12:32, 14 December 2009 diff hist +76 Main Page
- 12:32, 14 December 2009 diff hist +16 SardiNIA →Medical Sequencing Project
- 12:31, 14 December 2009 diff hist +65 SardiNIA
- 12:30, 14 December 2009 diff hist +992 N SardiNIA Created page with '== Key References == If you are looking to learn about the project, I strongly recommend that you read the following papers Pilia G, Chen WM, Scuteri A, Orru M, Albai G, Dei …'
- 15:09, 8 December 2009 diff hist +770 Mantra.cpp current
- 15:02, 8 December 2009 diff hist +1,800 N Mantra.cpp New page: '''Mantra.cpp''' provides useful functions handling inheritance vectors. A call to Mantra::Prepare() will first list all the meioses in a pedigree (which constitute an inheritance vect...
- 03:32, 26 November 2009 diff hist +53 N Utility Library Created page with ' Parameters.h StringHash.h StringMap.h' current
- 03:31, 26 November 2009 diff hist +12 StringMap.h current
- 03:30, 26 November 2009 diff hist +345 N StringMap.h Created page with ''''StringMap.h''' declares classes that allow one to store a list of strings and associated items. The list is stored in sorted fashion. Inserts and deletes can be quite expensiv…'
- 03:26, 26 November 2009 diff hist +224 Parameters.h current
- 03:22, 26 November 2009 diff hist +854 N Parameters.h Created page with '''Parameters.h'' is a header file that defines a series of classes that are useful for processing command line parameters. == Example Usage == <source lang="cpp"> #include "…'
- 11:30, 24 November 2009 diff hist -40 BamGenotypeCheck
- 11:29, 24 November 2009 diff hist +30 N Lanecheck moved Lanecheck to BamIdentityCheck: renamed lane check to bamIdentityCheck which is more descriptive current
- 11:29, 24 November 2009 diff hist 0 m BamGenotypeCheck moved Lanecheck to BamIdentityCheck: renamed lane check to bamIdentityCheck which is more descriptive
- 11:28, 24 November 2009 diff hist -23 TrioCaller Blanked the page
- 14:21, 20 November 2009 diff hist -9 Karma-colorspace →Additional Information
- 14:20, 20 November 2009 diff hist -30 Karma-colorspace
- 14:19, 20 November 2009 diff hist -31 Karma-colorspace →Build Binary Reference Genome and Word Index
- 22:37, 19 November 2009 diff hist +47 Karma
- 17:28, 19 November 2009 diff hist -22 VcfCodingSnps
- 17:27, 19 November 2009 diff hist +90 Main Page →Sequence Analysis Tools
- 17:17, 19 November 2009 diff hist 0 m VcfCodingSnps moved AnnoVcf to VcfCodingSnps: Better name
- 10:06, 18 November 2009 diff hist +64 FastQValidator →Valid FastQ File Requirements
- 10:05, 18 November 2009 diff hist +98 FastQValidator →Valid FastQ File Requirements
- 23:30, 16 November 2009 diff hist +573 N FastQValidator Created page with '== Status == The FastQ Validator is on our Todo List. == Valid FastQ File Requirements == A valid fastQ file should meet the following requirements: * A base sequence sho…'
- 10:43, 16 November 2009 diff hist -1 Karma-colorspace →Input file requirement
- 10:43, 16 November 2009 diff hist -38 Karma-colorspace →Input file requirement
- 10:40, 16 November 2009 diff hist +6 Main Page →Welcome!
- 10:38, 16 November 2009 diff hist +233 Main Page →Welcome!
- 02:10, 15 November 2009 diff hist +1 Main Page →Variant Calling
- 01:52, 15 November 2009 diff hist +190 Abecasis Lab
- 01:49, 15 November 2009 diff hist +1 Abecasis Lab →Former Doctoral Students
- 01:49, 15 November 2009 diff hist +81 Abecasis Lab
- 01:48, 15 November 2009 diff hist +10 Abecasis Lab →Current Members
- 01:47, 15 November 2009 diff hist +831 N Abecasis Lab Created page with '== Current Members == === Research Faculty === Hyun Min Kang === Research Fellows === Bingshan Li === Graduate Students === Wei Chen Jun Ding Youna Hu Elizabeth Jewell Yanm…'
- 01:36, 15 November 2009 diff hist +223 N Genome Analysis Wiki:About Created page with 'This wiki documents useful tools and protocols for genome analysis. It is maintained by the Abecasis Lab at the [http://www.umich.edu University of Michigan] [http://csg.sp…' current
- 01:32, 15 November 2009 diff hist +116 GlfTrio →TODO
- 01:31, 15 November 2009 diff hist +171 GlfSingle
- 01:30, 15 November 2009 diff hist +2,153 N GlfMultiples Created page with ''''glfMultiples''' is a GLF-based variant caller for next-generation sequencing data. It takes a set of GLF format genotype likelihood files as input and generates a [[VC…'
- 00:53, 15 November 2009 diff hist +103 GLF
- 00:51, 15 November 2009 diff hist +10 GlfTrio →Filtering According to Depth and Map Quality
- 00:51, 15 November 2009 diff hist +39 GlfTrio →Basic Usage Example
- 00:48, 15 November 2009 diff hist +152 GlfTrio →Basic Usage Example
- 00:45, 15 November 2009 diff hist 0 GlfTrio →Filtering According to Depth and Map Quality
- 00:45, 15 November 2009 diff hist 0 GlfTrio →Basic Output Options
- 00:44, 15 November 2009 diff hist 0 GlfTrio →X Chromosome Variant Calling
- 00:43, 15 November 2009 diff hist 0 GlfTrio →Sample Labels
- 00:43, 15 November 2009 diff hist -8 GlfTrio →Filtering According to Depth and Map Quality
- 00:43, 15 November 2009 diff hist -8 GlfTrio →Basic Output Options
- 00:42, 15 November 2009 diff hist +2,881 N GlfTrio Created page with ''''glfTrio''' is a GLF-based variant caller for next-generation sequencing data. It takes three GLF format genotype likelihood files as input and generates a VCF-form…'
- 00:04, 15 November 2009 diff hist -2 Main Page →Welcome!
- 19:02, 14 November 2009 diff hist +177 N VCF Created page with ''''VCF''' is the Variant Calling Format. For the current specification, see [http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcfv3.2 VCF format specification].'
- 19:00, 14 November 2009 diff hist +2 Main Page
- 18:59, 14 November 2009 diff hist +278 Main Page
- 18:55, 14 November 2009 diff hist +14 GLF →Last Record
- 18:54, 14 November 2009 diff hist +3,714 GLF
- 18:13, 14 November 2009 diff hist +962 GlfSingle
- 18:07, 14 November 2009 diff hist +556 N GLF Created page with ''''GLF''' is a format for storing marginal likelihoods for next-generation sequence data, conditional on a set of possible genotypes. === Generating GLF Files === GLF files can…'
- 17:59, 14 November 2009 diff hist +448 N GlfSingle Created page with ''''glfSingle''' is a GLF-based variant caller for next-generation sequencing data. It takes a GLF format genotype likelihood file as input and generates a VCF-format …'
- 17:44, 14 November 2009 diff hist +2 METAL Command Reference
- 17:43, 14 November 2009 diff hist +2,100 N METAL Command Reference Created page with '=== Describing Input Files === SEPARATOR [WHITESPACE|COMMA|BOTH|TAB] (default = WHITESPACE) COLUMNCOUNTING [STRICT|LENIENT] (default = 'STRICT') MARK…'
- 01:39, 14 November 2009 diff hist +1 Main Page
- 01:38, 14 November 2009 diff hist +7 Main Page
- 01:37, 14 November 2009 diff hist +2 Main Page
- 01:34, 14 November 2009 diff hist +59 Main Page
- 01:32, 14 November 2009 diff hist +40 N File:2009.08 Group Retreat Photo.jpg Photo from Group Retreat in August 2008.
- 13:52, 13 November 2009 diff hist +48 Karma
- 13:52, 13 November 2009 diff hist +25 N Karma Created page with 'Karma is top secret. Shh!'
- 13:51, 13 November 2009 diff hist +122 Main Page
- 02:19, 11 November 2009 diff hist +3 Main Page
- 02:18, 11 November 2009 diff hist -12 Main Page
- 02:18, 11 November 2009 diff hist -503 Main Page
- 02:17, 11 November 2009 diff hist +78 Main Page
- 02:16, 11 November 2009 diff hist +497 Main Page
- 02:15, 11 November 2009 diff hist +248 Main Page
- 01:38, 11 November 2009 diff hist -31 Main Page
- 01:37, 11 November 2009 diff hist +31 Main Page
- 01:30, 11 November 2009 diff hist 0 Main Page
- 11:52, 10 November 2009 diff hist -423 Main Page