User contributions
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Jump to navigationJump to search- 16:57, 17 December 2013 diff hist -2 Vt →Sorting
- 16:55, 17 December 2013 diff hist +368 Vt →Common options
- 14:19, 16 December 2013 diff hist 0 Vt →View
- 10:29, 16 December 2013 diff hist +53 Vt →Genotype
- 11:19, 13 December 2013 diff hist +84 Vt →Sorting
- 11:16, 13 December 2013 diff hist +56 Vt →VCF Manipulation
- 09:13, 13 December 2013 diff hist -33 Vt →View
- 18:44, 12 December 2013 diff hist -3 Vt →VCF Manipulation
- 18:44, 12 December 2013 diff hist +550 Vt →Merge duplicate variants
- 16:15, 5 December 2013 diff hist +9 Vt →Construct Probes
- 12:12, 5 December 2013 diff hist +24 Vt →VCF Manipulation
- 12:11, 5 December 2013 diff hist +8 Vt →Programs
- 10:33, 5 December 2013 diff hist -15 Vt →Construct Probes
- 10:33, 5 December 2013 diff hist -1 Vt →Merge candidate variants
- 10:33, 5 December 2013 diff hist +668 Vt →Merge candidate variants
- 09:57, 5 December 2013 diff hist +128 Vt →Genotype
- 09:52, 5 December 2013 diff hist +6 Vt →Merge candidate variants
- 09:51, 5 December 2013 diff hist +227 Vt →Merge candidate variants
- 20:50, 4 December 2013 diff hist +37 Vt →Installation
- 20:49, 4 December 2013 diff hist +117 Vt →Installation
- 20:46, 4 December 2013 diff hist -94 Vt →View
- 20:46, 4 December 2013 diff hist -282 Vt →Programs
- 20:45, 4 December 2013 diff hist -94 Vt →Merge candidate variants
- 20:45, 4 December 2013 diff hist -94 Vt →Discover
- 20:45, 4 December 2013 diff hist -15 Vt →Index
- 20:37, 4 December 2013 diff hist +489 Vt →View
- 16:21, 4 December 2013 diff hist +2 Vt →Discover
- 16:21, 4 December 2013 diff hist +26 Vt →Discover
- 16:20, 4 December 2013 diff hist +27 Vt →View
- 16:18, 4 December 2013 diff hist -17 Vt →View
- 16:17, 4 December 2013 diff hist +110 Vt →View
- 09:22, 4 December 2013 diff hist -177 Vt →Discover
- 09:21, 4 December 2013 diff hist +589 Vt →Discover
- 09:19, 4 December 2013 diff hist +2,420 Vt →Merge duplicate variants
- 17:27, 21 November 2013 diff hist +18 Vt →Installation
- 17:26, 21 November 2013 diff hist +1 Vt →Merge duplicate variants
- 17:25, 21 November 2013 diff hist -61 Vt →Merge duplicate variants
- 17:24, 21 November 2013 diff hist 0 Vt →Normalization
- 17:24, 21 November 2013 diff hist +60 Vt →Normalization
- 17:23, 21 November 2013 diff hist 0 Vt →Merge duplicate variants
- 11:39, 20 November 2013 diff hist -210 Vt →Merge duplicate variants
- 11:38, 20 November 2013 diff hist +375 Vt →Merge duplicate variants
- 11:33, 20 November 2013 diff hist -25 Vt →Merge duplicate variants
- 15:34, 18 November 2013 diff hist +125 Vt →Installation
- 17:22, 5 November 2013 diff hist 0 Vt →Common options
- 16:03, 5 November 2013 diff hist -2 Vt →Normalization
- 16:02, 5 November 2013 diff hist -5 Vt →Normalization
- 11:40, 5 November 2013 diff hist +1 Vt →Installation
- 11:39, 5 November 2013 diff hist +196 Vt →Location
- 11:36, 5 November 2013 diff hist +99 Vt →Normalization
- 17:36, 21 October 2013 diff hist +327 Vt →Normalization
- 17:21, 21 October 2013 diff hist +5 Vt →Normalization
- 17:19, 21 October 2013 diff hist -40 Vt →Normalization
- 17:17, 21 October 2013 diff hist +610 Vt →Normalization
- 16:38, 21 October 2013 diff hist +16 Vt
- 16:32, 21 October 2013 diff hist +100 Vt →Common options
- 16:27, 21 October 2013 diff hist +7 Vt →Normalization
- 16:26, 21 October 2013 diff hist +10 Vt →Location
- 16:26, 21 October 2013 diff hist +24 Vt →Common options
- 16:25, 21 October 2013 diff hist -7,518 Vt
- 16:25, 21 October 2013 diff hist +7 Vt →Normalization
- 16:24, 21 October 2013 diff hist -1 Variant Normalization →Implementation
- 16:24, 21 October 2013 diff hist -1 Variant Normalization →Implementation
- 16:17, 21 October 2013 diff hist +8,814 Vt
- 09:35, 13 July 2013 diff hist +1 Variant Normalization →Maintained by
- 09:35, 13 July 2013 diff hist -1 Variant Normalization →Maintained by
- 09:34, 13 July 2013 diff hist +102 Variant Normalization →Maintained by
- 09:31, 13 July 2013 diff hist 0 Variant Normalization →Normalization
- 09:30, 13 July 2013 diff hist -3 Variant Normalization →Normalization
- 09:30, 13 July 2013 diff hist +6 Variant Normalization →Introduction
- 09:30, 13 July 2013 diff hist +17 Variant Normalization →Normalization
- 09:29, 13 July 2013 diff hist +17 Variant Normalization →Normalization
- 09:28, 13 July 2013 diff hist +4 Variant Normalization →How to observe that a variant is not left aligned or parsimonious on the right side?
- 09:28, 13 July 2013 diff hist -4 Variant Normalization →Algorithm for Normalization
- 18:20, 12 July 2013 diff hist -2 Variant Normalization →Left alignment
- 18:19, 12 July 2013 diff hist +2 Variant Normalization →Left alignment
- 18:19, 12 July 2013 diff hist +146 Variant Normalization →Left alignment
- 18:16, 12 July 2013 diff hist -2 Variant Normalization →Left alignment
- 18:14, 12 July 2013 diff hist +22 Variant Normalization →How to observe that a variant is not left aligned or parsimonious on the right side?
- 17:32, 12 July 2013 diff hist 0 File:Variant normalization algorithm.png uploaded a new version of "File:Variant normalization algorithm.png" current
- 17:31, 12 July 2013 diff hist -74 Variant Normalization →How to observe that a variant is not left aligned or parsimonious on the right side?
- 17:27, 12 July 2013 diff hist -109 Variant Normalization →Algorithm for Normalization
- 17:25, 12 July 2013 diff hist 0 File:Variant normalization algorithm.png uploaded a new version of "File:Variant normalization algorithm.png"
- 17:20, 12 July 2013 diff hist -18 Variant Normalization →How to observe that a variant is not left aligned or parsimonious on the right side?
- 17:18, 12 July 2013 diff hist +2 Variant Normalization →Proof of property
- 17:18, 12 July 2013 diff hist -15 Variant Normalization →Proof of left alignment property
- 17:17, 12 July 2013 diff hist 0 Variant Normalization →Left alignment
- 17:15, 12 July 2013 diff hist 0 Variant Normalization
- 17:04, 12 July 2013 diff hist +391 Variant Normalization →Normalization
- 16:46, 12 July 2013 diff hist +3 Variant Normalization →Normalization
- 16:45, 12 July 2013 diff hist 0 N File:Normalization str.png
- 16:45, 12 July 2013 diff hist 0 N File:Normalization mnp.png
- 15:17, 11 July 2013 diff hist +85 Variant Normalization →Algorithm for Normalization
- 15:52, 9 July 2013 diff hist +61 Variant Normalization →Left alignment
- 15:51, 9 July 2013 diff hist 0 Variant Normalization →Algorithm for Normalization
- 15:50, 9 July 2013 diff hist -115 Variant Normalization →Algorithm for Normalization
- 15:44, 9 July 2013 diff hist 0 File:Variant normalization algorithm.png uploaded a new version of "File:Variant normalization algorithm.png"
- 15:41, 9 July 2013 diff hist +80 Variant Normalization →Algorithm for Normalization
- 15:41, 9 July 2013 diff hist -11 Variant Normalization →Proof of left alignment
- 15:35, 9 July 2013 diff hist +34 Variant Normalization →How to observe that a variant is not left aligned or parsimonious on the right side?
- 15:33, 9 July 2013 diff hist +34 Variant Normalization →How to observe that a variant is not left aligned?
- 15:13, 9 July 2013 diff hist -2 Variant Normalization →Normalization
- 15:12, 9 July 2013 diff hist +292 Variant Normalization
- 15:11, 9 July 2013 diff hist +4 Variant Normalization
- 15:10, 9 July 2013 diff hist 0 Left alignment Redirected page to Variant Normalization current
- 15:09, 9 July 2013 diff hist +35 N Left alignment Redirected page to Variant normalization
- 15:08, 9 July 2013 diff hist +3,110 N Variant Normalization Created page with '= Introduction = Variant representation in Variant Call Format is non unique. We describe a variant normalization here that is parsimonious and left aligned. = Normalization =…'
- 14:43, 9 July 2013 diff hist 0 N File:Variant normalization algorithm.png
- 14:32, 9 July 2013 diff hist 0 N File:Left alignment.png current
- 14:28, 9 July 2013 diff hist 0 N File:Left alignment.pdf current
- 13:40, 4 June 2013 diff hist -1,681 HWEP Redirected page to Genotype Likelihood based Hardy-Weinberg Test current
- 13:38, 4 June 2013 diff hist -2,329 AF Redirected page to Genotype Likelihood based Allele Frequency current
- 13:37, 4 June 2013 diff hist -5 Genotype Likelihood based Inbreeding Coefficient →Introduction
- 13:36, 4 June 2013 diff hist -2 Genotype Likelihood based Inbreeding Coefficient →Introduction
- 13:32, 4 June 2013 diff hist +1,858 N Genotype Likelihood based Hardy-Weinberg Test Created page with '=== Introduction === This page details a Hardy-Weinberg Equilibrium test based on genotype likelihoods in NGS data. === Formulation === Hardy Weinberg equilibrium is expected …'
- 13:30, 4 June 2013 diff hist -3 Genotype Likelihood based Allele Frequency →Introduction
- 13:22, 4 June 2013 diff hist +2,213 N Genotype Likelihood based Inbreeding Coefficient Created page with '=== Introduction === Inbreeding Coefficients are an important statistic in the study of genetic variants. This page details EM algorithms to estimate inbreeding coefficients fro…'
- 13:21, 4 June 2013 diff hist -35 FIC Redirected page to Genotype Likelihood based Inbreeding Coefficient current
- 13:20, 4 June 2013 diff hist -1,901 FIC Redirected page to Https://statgen.sph.umich.edu/wiki/Genotype Likelihood based Inbreeding Coefficient
- 13:13, 4 June 2013 diff hist +2,589 N Genotype Likelihood based Allele Frequency Created page with '=== Introduction === Allele frequencies are an important statistic in the study of genetic variants. This page details EM algorithms to estimate allele frequencies from genoty…'
- 12:36, 18 May 2013 diff hist -3,263 Vt Blanked the page
- 14:17, 11 April 2013 diff hist +29 FIC →Formulation
- 14:16, 11 April 2013 diff hist +212 FIC →Formulation
- 14:13, 11 April 2013 diff hist +22 FIC
- 14:05, 11 April 2013 diff hist -1 FIC
- 14:05, 11 April 2013 diff hist -27 HWEP →Derivation
- 14:04, 11 April 2013 diff hist -4 AF →Derivation by
- 14:03, 11 April 2013 diff hist +104 AF →Derivation by
- 14:02, 11 April 2013 diff hist +11 AF →Estimation of Genotype Frequencies without assuming HWE
- 14:01, 11 April 2013 diff hist +66 AF →Estimation of Genotype Frequencies without assuming HWE
- 13:55, 11 April 2013 diff hist +14 FIC
- 13:35, 11 April 2013 diff hist -22 HWEP →Maintained by
- 13:34, 11 April 2013 diff hist +54 HWEP →Maintained by
- 13:34, 11 April 2013 diff hist +31 AF
- 13:33, 11 April 2013 diff hist -1 FIC
- 11:05, 11 April 2013 diff hist +20 AF →Estimation of Genotype Frequencies without assuming HWE
- 11:04, 11 April 2013 diff hist +21 HWEP
- 11:03, 11 April 2013 diff hist -8 HWEP
- 10:58, 11 April 2013 diff hist +1,722 N HWEP Created page with 'Hardy Weinberg equilibrium is expected in a panmictic population. The following formulation is a likelihood ratio test statistic that incorporates the genotype uncertainty via g…'
- 10:31, 11 April 2013 diff hist +110 FIC
- 10:30, 11 April 2013 diff hist +2,157 N AF Created page with '=== Estimation of Genotype Frequencies without assuming HWE === We propose an EM algorithm to estimate the genotype frequencies without assuming HWE. The posterior probability …'
- 08:31, 11 April 2013 diff hist +1,613 N FIC Created page with 'Many data sets consist of individuals from different populations, in the cases of structured populations, this usually result in an increased number of homozygotes. The inbreedi…'
- 21:23, 12 March 2013 diff hist +1 Vt →Left Alignment
- 16:58, 12 March 2013 diff hist +2 Vt →Filtering
- 16:55, 12 March 2013 diff hist +93 Vt →Compute Feature
- 16:53, 12 March 2013 diff hist +33 Vt →Filtering
- 16:33, 12 March 2013 diff hist +489 Vt →Discovery
- 16:26, 12 March 2013 diff hist -4 Vt
- 16:22, 12 March 2013 diff hist +116 Vt →compute_
- 16:19, 12 March 2013 diff hist +133 Vt →Introduction
- 16:18, 12 March 2013 diff hist +588 Vt →Left Alignment
- 16:11, 12 March 2013 diff hist +1,812 N Vt Created page with '=== Introduction === vt is a tool set that calls, genotypes and filters short variants. It provides profiling of variants to aid in QC. === Discovery === Discovery is perform…'
- 15:12, 2 November 2012 diff hist +53 N IGFPipe Created page with 'IGFPipe Pipeline for INDEL Genotyping and Filtering' current
- 18:38, 2 February 2012 diff hist +209 Arf →In development/Pending update current
- 18:26, 2 February 2012 diff hist +15 Arf →In development
- 18:23, 2 February 2012 diff hist -11 Arf →In development
- 18:19, 2 February 2012 diff hist -15 Arf →In development
- 18:19, 2 February 2012 diff hist +15 Arf →In development
- 18:18, 2 February 2012 diff hist -12 Arf →In development
- 18:16, 2 February 2012 diff hist +42 Arf →In development
- 18:15, 2 February 2012 diff hist +219 Arf →In development
- 17:05, 27 January 2012 diff hist -3 Arf →Download
- 17:04, 27 January 2012 diff hist +9 Arf →Download
- 15:47, 27 January 2012 diff hist -189 Arf →In development
- 14:35, 27 January 2012 diff hist +80 Arf →In development
- 14:34, 27 January 2012 diff hist +57 Arf →In development
- 14:28, 27 January 2012 diff hist +308 Arf →Command Line Options
- 13:46, 27 January 2012 diff hist +31 Arf →Command Line Options
- 23:37, 25 January 2012 diff hist -1 Arf →Basic Usage Example
- 23:36, 25 January 2012 diff hist +1 Arf →Basic Usage Example
- 23:36, 25 January 2012 diff hist +152 Arf →Basic Usage Example
- 23:35, 25 January 2012 diff hist +392 Arf →Basic Usage Example
- 21:31, 25 January 2012 diff hist +1 Arf →Basic Usage Example
- 20:01, 25 January 2012 diff hist +30 Arf →Command Line Options
- 18:15, 25 January 2012 diff hist +177 Arf →Download
- 18:02, 25 January 2012 diff hist -59 Arf →Description
- 18:02, 25 January 2012 diff hist +58 Arf →Command Line Options
- 18:01, 25 January 2012 diff hist +17 Arf →Basic Usage Example
- 15:07, 24 January 2012 diff hist -4 Arf →Basic Usage Example
- 21:33, 23 January 2012 diff hist +1 Arf →Basic Usage Example
- 21:32, 23 January 2012 diff hist -168 Arf →Basic Usage Example
- 21:32, 23 January 2012 diff hist -33 Arf →Basic Usage Example
- 21:30, 23 January 2012 diff hist +54 Arf →Command Line Options
- 21:29, 23 January 2012 diff hist -19 Arf →Output
- 17:15, 23 January 2012 diff hist +343 Arf →Basic Usage Example
- 17:12, 23 January 2012 diff hist 0 Arf →Command Line Options
- 17:11, 23 January 2012 diff hist +4 Arf →Download
- 17:11, 23 January 2012 diff hist +4 Vmatch →Download current
- 16:58, 23 January 2012 diff hist -51 Vmatch →Download
- 16:54, 23 January 2012 diff hist -48 Arf →Download
- 11:48, 19 January 2012 diff hist -74 Vpeep →Output current
- 11:48, 19 January 2012 diff hist +1 Vpeep →Output
- 11:48, 19 January 2012 diff hist +1 Vpeep →Output
- 11:48, 19 January 2012 diff hist +206 Vpeep →Output
- 11:47, 19 January 2012 diff hist +2,317 N Vpeep Created page with 'Category:Software '''vpeep''' checks the distribution in a VCF file. == Basic Usage Example == vpeep <vcf-file> example: vpeep pscalare.vcf == Output == user…'
- 18:35, 18 January 2012 diff hist -23 Arf →Output
- 11:41, 18 January 2012 diff hist 0 Arf →Output
- 11:40, 18 January 2012 diff hist -31 Arf →Command Line Options
- 11:40, 18 January 2012 diff hist 0 Arf →Basic Usage Example
- 11:40, 18 January 2012 diff hist 0 Arf →Basic Usage Example
- 18:38, 17 January 2012 diff hist -1 Arf →Basic Usage Example
- 18:38, 17 January 2012 diff hist -202 Arf →Basic Usage Example
- 18:37, 17 January 2012 diff hist +56 Vmatch →Download
- 17:06, 17 January 2012 diff hist +36 Arf →Command Line Options
- 17:06, 17 January 2012 diff hist +128 Arf →Output
- 17:04, 17 January 2012 diff hist -367 Arf →Description
- 17:02, 17 January 2012 diff hist +121 Arf →Command Line Options
- 17:00, 17 January 2012 diff hist +555 Arf →Basic Usage Example
- 16:55, 17 January 2012 diff hist -126 Arf →Command Line Options
- 16:54, 17 January 2012 diff hist +363 Arf →Basic Usage Example
- 16:49, 17 January 2012 diff hist +472 Arf →Basic Usage Example
- 17:02, 16 January 2012 diff hist +124 Arf →Command Line Options
- 17:00, 16 January 2012 diff hist -3 Arf →Download
- 16:59, 16 January 2012 diff hist +1,619 N Arf Created page with 'Category:Software '''arf''' is a genetic analysis program for sequencing data. == Basic Usage Example == arf [options] <vcf-file> Here is an example of how <code>arf</co…'
- 16:42, 16 January 2012 diff hist -3 Vmatch →Output
- 16:01, 16 January 2012 diff hist -105 Vmatch →Output
- 16:00, 16 January 2012 diff hist +552 Vmatch →Output
- 15:48, 16 January 2012 diff hist +104 Vmatch →Command Line Options
- 15:46, 16 January 2012 diff hist -1 Vmatch →Output
- 15:45, 16 January 2012 diff hist +1 Vmatch →Output
- 15:45, 16 January 2012 diff hist +111 Vmatch →Output
- 15:44, 16 January 2012 diff hist +241 Vmatch →Output
- 15:41, 16 January 2012 diff hist +524 Vmatch →Output
- 15:34, 16 January 2012 diff hist +2 Vmatch →Command Line Options
- 15:34, 16 January 2012 diff hist -6 Vmatch →Command Line Options
- 15:33, 16 January 2012 diff hist +90 Vmatch →Command Line Options
- 15:31, 16 January 2012 diff hist -50 Vmatch →Download
- 15:31, 16 January 2012 diff hist +186 Vmatch →Download
- 15:29, 16 January 2012 diff hist +65 Vmatch →Download
- 15:26, 16 January 2012 diff hist +55 Vmatch →Download
- 15:26, 16 January 2012 diff hist +51 Vmatch →Download
- 15:24, 16 January 2012 diff hist +66 Vmatch →Download
- 15:01, 16 January 2012 diff hist -60 Vmatch →Download
- 11:34, 16 January 2012 diff hist -2 Vmatch →Output
- 11:34, 16 January 2012 diff hist -35 Vmatch →Output
- 11:34, 16 January 2012 diff hist -93 Vmatch →Output
- 11:33, 16 January 2012 diff hist -120 Vmatch →Output
- 11:30, 16 January 2012 diff hist +253 Vmatch →Output
- 11:30, 16 January 2012 diff hist -85 Vmatch →Output
- 11:29, 16 January 2012 diff hist +42 Vmatch →Output
- 11:27, 16 January 2012 diff hist +1,207 Vmatch →Output
- 11:13, 16 January 2012 diff hist +104 Vmatch →Command Line Options
- 11:12, 16 January 2012 diff hist +16 Vmatch →Description
- 11:10, 16 January 2012 diff hist -171 Vmatch →TODO
- 11:05, 16 January 2012 diff hist +4 Vmatch →Description
- 11:04, 16 January 2012 diff hist +2,023 N Vmatch Created page with 'Category:Software '''vmatch''' is a variant matching program for MNPs, INDELs and precise SVs in VCF files. == Basic Usage Example == vmatch <vcf-file-1> <vcf-file-2>…'
- 14:48, 7 January 2011 diff hist 0 C++ Class: InputFile →Example
- 12:48, 7 September 2010 diff hist -189 Biostatistics 666: Main Page →Class Notes
- 12:47, 7 September 2010 diff hist +1 Biostatistics 666: Main Page →Class Notes
- 12:47, 7 September 2010 diff hist +188 Biostatistics 666: Main Page →Class Notes