User contributions
From Genome Analysis Wiki
Jump to navigationJump to search- 16:15, 7 May 2014 diff hist +864 Vt →Filters
- 16:12, 7 May 2014 diff hist +58 Vt →Filters
- 08:37, 28 April 2014 diff hist -11 Vt →Compute Features
- 08:36, 28 April 2014 diff hist +1,136 Vt →Annotate Variants
- 17:33, 14 April 2014 diff hist 0 File:Normalization mnp.png Atks uploaded a new version of "File:Normalization mnp.png" current
- 17:32, 14 April 2014 diff hist 0 File:Normalization mnp.png Atks uploaded a new version of "File:Normalization mnp.png"
- 11:45, 27 March 2014 diff hist +9 Vt →Updating
- 11:45, 27 March 2014 diff hist +76 Vt →Updating
- 21:10, 28 February 2014 diff hist -1 Vt →Annotate Variants
- 21:09, 28 February 2014 diff hist +82 Vt →Updating
- 21:09, 28 February 2014 diff hist +8 Vt →Updating
- 21:08, 28 February 2014 diff hist +127 Vt →Installation
- 21:06, 28 February 2014 diff hist -139 Vt →Annotate Variants
- 21:06, 28 February 2014 diff hist +14 Vt →Annotate Variants
- 21:05, 28 February 2014 diff hist +26 Vt →Annotate Variants
- 21:05, 28 February 2014 diff hist +82 Vt →Resource Bundle
- 21:02, 28 February 2014 diff hist +9 Vt →Annotate Variants
- 18:23, 20 February 2014 diff hist +47 Analyses of Indels →Insertion/Deletion ratios, Coding Regions and Overlap analysis
- 18:19, 20 February 2014 diff hist +28 Analyses of Indels →to document
- 18:16, 20 February 2014 diff hist +261 Analyses of Indels →Insertion/Deletion ratios, Coding Regions and Overlap analysis
- 18:10, 20 February 2014 diff hist +304 Analyses of Indels →Insertion/Deletion ratios, Coding Regions and Overlap analysis
- 18:06, 20 February 2014 diff hist +75 Analyses of Indels →Insertion/Deletion ratios, Coding Regions and Overlap analysis
- 18:01, 20 February 2014 diff hist +37 Analyses of Indels →Insertion/Deletion ratios, Coding Regions and Overlap analysis
- 16:45, 20 February 2014 diff hist -398 Analyses of Indels
- 16:42, 20 February 2014 diff hist +113 Analyses of Indels →Insertion/Deletion ratios, Coding Regions and Overlap analysis
- 16:40, 20 February 2014 diff hist +1,495 Analyses of Indels →Insertion/Deletion ratios, Coding Regions and Overlap analysis
- 16:31, 20 February 2014 diff hist +48 Analyses of Indels →Coding regions
- 16:27, 20 February 2014 diff hist +629 Analyses of Indels →Coding regions
- 16:22, 20 February 2014 diff hist +794 Analyses of Indels →Normalization
- 16:19, 20 February 2014 diff hist +212 Analyses of Indels →Coding regions
- 16:17, 20 February 2014 diff hist +57 Analyses of Indels →Normalization
- 16:15, 20 February 2014 diff hist +464 Analyses of Indels →Normalization
- 16:10, 20 February 2014 diff hist +110 Analyses of Indels →Peek
- 15:38, 20 February 2014 diff hist +876 Analyses of Indels →Analyses
- 15:27, 20 February 2014 diff hist +864 Analyses of Indels →Analyses
- 15:01, 20 February 2014 diff hist +57 Analyses of Indels →Coding regions
- 15:29, 19 February 2014 diff hist 0 Analyses of Indels →Normalization
- 15:26, 19 February 2014 diff hist +12 Analyses of Indels
- 15:26, 19 February 2014 diff hist +5 Analyses of Indels
- 15:25, 19 February 2014 diff hist +6 Analyses of Indels →Tools
- 15:24, 19 February 2014 diff hist -18 Analyses of Indels →Motivation
- 15:19, 19 February 2014 diff hist -1 Variant Normalization →Parsimony
- 15:18, 19 February 2014 diff hist +55 Analyses of Indels →Normalization
- 15:17, 19 February 2014 diff hist +11 Analyses of Indels →Normalization
- 15:15, 19 February 2014 diff hist +743 Analyses of Indels →Normalization
- 15:08, 19 February 2014 diff hist +5 Analyses of Indels →Normalization
- 15:07, 19 February 2014 diff hist +566 Analyses of Indels →Normalization
- 12:16, 19 February 2014 diff hist +1,363 N Analyses of Indels Created page with "=Motivation= This wiki page will details the useful steps in analysing Indels. In particular it is to help the group in understanding the issues and perform the analyses qui..."
- 16:04, 18 February 2014 diff hist 0 Vt →Profile Indels
- 16:03, 18 February 2014 diff hist -14 Vt →Profile Indels
- 10:12, 18 February 2014 diff hist -131 Vt →Installation
- 16:18, 13 February 2014 diff hist +9 Vt →Filters
- 15:48, 13 February 2014 diff hist +160 Vt →Filters
- 15:46, 13 February 2014 diff hist -2 Vt →Filters
- 15:46, 13 February 2014 diff hist -2 Vt →Filters
- 15:45, 13 February 2014 diff hist -61 Vt →Filters
- 17:31, 4 February 2014 diff hist +669 Vt →Uncompressed BCF streams
- 16:29, 30 January 2014 diff hist +103 Vt →Profile Indels
- 14:23, 30 January 2014 diff hist +15 Vt →Profile NA12878
- 14:20, 30 January 2014 diff hist +1,034 Vt →Profile NA12878
- 14:20, 30 January 2014 diff hist -1,035 Vt →Profile Mendelian Errors
- 14:20, 30 January 2014 diff hist +1,035 Vt →Profile Mendelian Errors
- 14:14, 30 January 2014 diff hist +2,079 Vt →Profile Mendelian Errors
- 16:36, 29 January 2014 diff hist +4 Vt →Inspection and Evaluation
- 16:35, 29 January 2014 diff hist +29 Vt →Peek
- 16:34, 29 January 2014 diff hist +2 Vt →VCF Manipulation
- 16:33, 29 January 2014 diff hist +62 Vt →Concatenate
- 15:45, 29 January 2014 diff hist +5 Vt →Profile Mendelian Errors
- 15:44, 29 January 2014 diff hist -1 Vt →Profile Mendelian Errors
- 15:44, 29 January 2014 diff hist +20 Vt →Profile Mendelian Errors
- 15:44, 29 January 2014 diff hist +6 Vt →Profile Mendelian Errors
- 15:42, 29 January 2014 diff hist 0 N File:Mendel.pdf current
- 15:41, 29 January 2014 diff hist +15 Vt →Profile Mendelian Errors
- 15:39, 29 January 2014 diff hist +99 Vt →Profile Mendelian Errors
- 15:34, 29 January 2014 diff hist -127 Vt →Profile Mendelian Errors
- 15:21, 29 January 2014 diff hist +2,869 Vt →Profile Indels
- 09:36, 29 January 2014 diff hist +622 Vt →VCF Manipulation
- 12:27, 24 January 2014 diff hist +553 Vt →Annotate Variants
- 12:15, 24 January 2014 diff hist +557 Vt →Peek
- 12:03, 24 January 2014 diff hist +1,396 Vt →Profile Indels
- 12:00, 24 January 2014 diff hist +197 Vt →Profile Indels
- 11:57, 24 January 2014 diff hist +746 Vt →Profile Indels
- 11:49, 24 January 2014 diff hist +1,968 Vt →Peek
- 16:12, 23 January 2014 diff hist +7 Vt →Installation
- 15:43, 23 January 2014 diff hist -179 Vt →Normalization
- 15:35, 23 January 2014 diff hist -130 Vt →Normalization
- 15:32, 23 January 2014 diff hist +964 Vt →Normalization
- 15:25, 23 January 2014 diff hist -12 Vt →Normalization
- 14:55, 23 January 2014 diff hist +109 Vt →Normalization
- 14:51, 23 January 2014 diff hist +332 Vt →Normalization
- 13:33, 23 January 2014 diff hist -15 Vt →Normalization
- 13:31, 23 January 2014 diff hist +127 Vt →Installation
- 18:30, 14 January 2014 diff hist +519 Vt →Peek
- 08:19, 10 January 2014 diff hist -18 Vt →Peek
- 17:51, 7 January 2014 diff hist +10 Vt
- 17:35, 3 January 2014 diff hist +143 Vt →View
- 13:21, 3 January 2014 diff hist +82 Vt →Common options
- 13:19, 3 January 2014 diff hist +25 Vt →Uncompressed BCF streams
- 15:42, 2 January 2014 diff hist -1 Vt →Uncompressed BCF streams
- 15:41, 2 January 2014 diff hist +8 Vt →Uncompressed BCF streams
- 15:38, 2 January 2014 diff hist -9 Vt →Uncompressed BCF streams
- 15:38, 2 January 2014 diff hist +621 Vt →Alternate headers
- 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