User contributions for Albrecht

4 December 2015

• 11:2711:27, 4 December 2015 diff hist +234‎ Input ‎No edit summary
• 11:2211:22, 4 December 2015 diff hist +12‎ Input ‎No edit summary
• 11:2011:20, 4 December 2015 diff hist −367‎ Quick Start ‎No edit summary
• 11:1911:19, 4 December 2015 diff hist −161‎ Quick Start ‎ →‎Examples
• 10:5610:56, 4 December 2015 diff hist +12‎ Quick Start ‎ →‎Ancestral fasta file for hg19
• 10:5210:52, 4 December 2015 diff hist +33‎ Quick Start ‎No edit summary
• 10:4910:49, 4 December 2015 diff hist −92‎ MediaWiki:Sitenotice ‎No edit summary

19 November 2015

• 17:1317:13, 19 November 2015 diff hist +35‎ MediaWiki:Sidebar ‎No edit summary

12 November 2015

• 20:1920:19, 12 November 2015 diff hist +103‎ MsToGlf ‎No edit summary

11 July 2015

• 15:5115:51, 11 July 2015 diff hist +811‎ Contamination ‎No edit summary current

28 June 2015

• 14:0114:01, 28 June 2015 diff hist +1‎ Plink ‎No edit summary

5 April 2015

• 19:5219:52, 5 April 2015 diff hist +318‎ Genotype calling ‎ →‎options

15 December 2014

• 19:5019:50, 15 December 2014 diff hist −8‎ SYKmaf ‎ Undo revision 2344 by Albrecht (talk) current
• 19:4919:49, 15 December 2014 diff hist +8‎ SYKmaf ‎ →‎ML estimator with unknown minor

25 August 2014

• 13:5813:58, 25 August 2014 diff hist −566‎ Association ‎ →‎Output
• 13:5613:56, 25 August 2014 diff hist +228‎ Association ‎ →‎Score statistic
• 13:4913:49, 25 August 2014 diff hist +201‎ Change log ‎ →‎Latest

27 June 2014

• 14:3514:35, 27 June 2014 diff hist −1,005‎ Contamination ‎ →‎method
• 14:3514:35, 27 June 2014 diff hist +1,005‎ N Rasmussen2011 ‎ Created page with "[http://www.ncbi.nlm.nih.gov/entrez?Db=pubmed&Cmd=ShowDetailView&uid=21940856 PMID 21940856], [http://www.bioinformatics.org/texmed/cgi-bin/list.cgi?PMID=21940856 bibtex ] Ras..." current
• 14:3414:34, 27 June 2014 diff hist +59‎ Citing angsd ‎No edit summary
• 14:3214:32, 27 June 2014 diff hist +174‎ Orlando2013 ‎No edit summary current
• 14:2914:29, 27 June 2014 diff hist +1,084‎ Contamination ‎No edit summary
• 14:0614:06, 27 June 2014 diff hist +35‎ Contamination ‎No edit summary
• 13:5913:59, 27 June 2014 diff hist +401‎ Contamination ‎ →‎Output

26 June 2014

• 13:2213:22, 26 June 2014 diff hist +14‎ Thetas,Tajima,Neutrality tests ‎ →‎Example
• 13:1813:18, 26 June 2014 diff hist −65‎ Thetas,Tajima,Neutrality tests ‎ →‎Example
• 13:1613:16, 26 June 2014 diff hist +203‎ Thetas,Tajima,Neutrality tests ‎ →‎Example
• 12:4512:45, 26 June 2014 diff hist +131‎ Major Minor ‎No edit summary
• 12:4212:42, 26 June 2014 diff hist +53‎ Major Minor ‎ →‎Pre specified Major using a reference
• 12:4112:41, 26 June 2014 diff hist −1‎ Major Minor ‎ →‎Pre specified Major using a reference
• 12:3412:34, 26 June 2014 diff hist −34‎ User:Albrecht ‎ Blanked the page current

24 June 2014

• 12:4612:46, 24 June 2014 diff hist +3‎ Input ‎ →‎Brief Overview

13 May 2014

• 17:1517:15, 13 May 2014 diff hist +556‎ Genotype Likelihoods ‎ →‎Output

23 April 2014

• 16:1916:19, 23 April 2014 diff hist +190‎ Major Minor ‎No edit summary
• 16:1616:16, 23 April 2014 diff hist −111‎ MediaWiki:Sitenotice ‎No edit summary
• 16:1516:15, 23 April 2014 diff hist +12‎ ANGSD ‎No edit summary

6 March 2014

• 13:2613:26, 6 March 2014 diff hist −8‎ SFS Estimation ‎ →‎How to plot
• 13:2513:25, 6 March 2014 diff hist −6‎ SFS Estimation ‎ →‎How to plot
• 13:2513:25, 6 March 2014 diff hist −19‎ SFS Estimation ‎ →‎Format specification of binary .saf file
• 13:2113:21, 6 March 2014 diff hist −56‎ SFS Estimation ‎ →‎Folded spectra
• 13:1613:16, 6 March 2014 diff hist +49‎ SFS Estimation ‎ →‎Interpretation of the emOptim2 output file
• 13:1513:15, 6 March 2014 diff hist +347‎ SFS Estimation ‎ →‎Options
• 12:2712:27, 6 March 2014 diff hist +148‎ SFS Estimation ‎ →‎Options
• 12:2612:26, 6 March 2014 diff hist +52‎ SFS Estimation ‎ →‎Posterior per-site distributions of the sample allele frequency
• 12:2312:23, 6 March 2014 diff hist +13‎ SFS Estimation ‎ →‎Interpretation of output file
• 12:2312:23, 6 March 2014 diff hist +47‎ SFS Estimation ‎ →‎Interpretation of output file
• 12:2012:20, 6 March 2014 diff hist −3‎ SFS Estimation ‎ →‎Example
• 12:2012:20, 6 March 2014 diff hist +155‎ SFS Estimation ‎ →‎Example
• 12:1812:18, 6 March 2014 diff hist +188‎ SFS Estimation ‎ →‎Brief Overview
• 12:1712:17, 6 March 2014 diff hist −64‎ SFS Estimation ‎ →‎Example
• 12:1612:16, 6 March 2014 diff hist +98‎ SFS Estimation ‎ →‎Example
• 12:1512:15, 6 March 2014 diff hist −1‎ SFS Estimation ‎ →‎Example
• 12:1112:11, 6 March 2014 diff hist +1‎ SFS Estimation ‎ →‎How to plot
• 12:1012:10, 6 March 2014 diff hist +43‎ SFS Estimation ‎ →‎How to plot
• 12:0912:09, 6 March 2014 diff hist −2,070‎ SFS Estimation ‎ →‎Theory
• 12:0912:09, 6 March 2014 diff hist −11‎ RealSFSmethod ‎ →‎Theory
• 12:0812:08, 6 March 2014 diff hist +2,068‎ N RealSFSmethod ‎ Created page with "=Theory= <pre> We will try to elaborate on the theory behind the methods. Below is only a preliminary version of the theory. </pre> This method is described in Nielsen2012..."
• 12:0812:08, 6 March 2014 diff hist +6‎ SFS Estimation ‎No edit summary
• 12:0812:08, 6 March 2014 diff hist +2‎ SFS Estimation ‎No edit summary
• 12:0812:08, 6 March 2014 diff hist +64‎ SFS Estimation ‎No edit summary
• 12:0612:06, 6 March 2014 diff hist +161‎ SFS Estimation ‎ →‎Options
• 12:0312:03, 6 March 2014 diff hist +67‎ SFS Estimation ‎No edit summary
• 11:5311:53, 6 March 2014 diff hist −9‎ Thetas,Tajima,Neutrality tests ‎ →‎Example
• 11:5211:52, 6 March 2014 diff hist −9‎ Thetas,Tajima,Neutrality tests ‎ →‎Unknown ancestral state (folded sfs)
• 11:5211:52, 6 March 2014 diff hist +4‎ Thetas,Tajima,Neutrality tests ‎ →‎Unknown ancestral state (folded sfs)
• 11:5111:51, 6 March 2014 diff hist +4‎ Thetas,Tajima,Neutrality tests ‎ →‎Unknown ancestral state (folded sfs)
• 11:5011:50, 6 March 2014 diff hist −4‎ Thetas,Tajima,Neutrality tests ‎ →‎Example
• 11:5011:50, 6 March 2014 diff hist +16‎ Thetas,Tajima,Neutrality tests ‎ →‎Unknown ancestral state (folded sfs)
• 11:4611:46, 6 March 2014 diff hist +26‎ Thetas,Tajima,Neutrality tests ‎ →‎Unknown ancestral state (folded sfs)
• 11:4411:44, 6 March 2014 diff hist +170‎ Thetas,Tajima,Neutrality tests ‎ →‎Unknown ancestral state (folded sfs)
• 11:4011:40, 6 March 2014 diff hist +33‎ Thetas,Tajima,Neutrality tests ‎ →‎Sliding Window example
• 11:3811:38, 6 March 2014 diff hist +129‎ Thetas,Tajima,Neutrality tests ‎ →‎.thetas.gz is
• 11:3711:37, 6 March 2014 diff hist +67‎ Thetas,Tajima,Neutrality tests ‎ →‎Example
• 11:3611:36, 6 March 2014 diff hist −18‎ Thetas,Tajima,Neutrality tests ‎ →‎Sliding Window example
• 11:2711:27, 6 March 2014 diff hist +1‎ Thetas,Tajima,Neutrality tests ‎ →‎Example
• 11:2511:25, 6 March 2014 diff hist +72‎ Thetas,Tajima,Neutrality tests ‎ →‎Example
• 11:0911:09, 6 March 2014 diff hist +39‎ Thetas,Tajima,Neutrality tests ‎ →‎Example

5 March 2014

• 20:1520:15, 5 March 2014 diff hist +1‎ Filters ‎ →‎Extra
• 20:1420:14, 5 March 2014 diff hist +16‎ Plink ‎ →‎Example
• 20:1220:12, 5 March 2014 diff hist −11‎ Filters ‎ →‎Extra
• 20:1220:12, 5 March 2014 diff hist −2‎ Plink ‎ →‎Example
• 20:0920:09, 5 March 2014 diff hist 0‎ Plink ‎No edit summary
• 20:0820:08, 5 March 2014 diff hist 0‎ Plink ‎ →‎Example
• 20:0120:01, 5 March 2014 diff hist −5‎ Plink ‎No edit summary
• 20:0020:00, 5 March 2014 diff hist +38‎ MediaWiki:Sidebar ‎No edit summary
• 19:3819:38, 5 March 2014 diff hist +29‎ Association ‎ →‎Example with imputation (using BEAGLE)
• 19:3619:36, 5 March 2014 diff hist +556‎ Association ‎ →‎Example with imputation (using BEAGLE)
• 19:3519:35, 5 March 2014 diff hist +279‎ Input ‎ →‎Genotype Probability Files
• 19:1819:18, 5 March 2014 diff hist −998‎ Bugs ‎No edit summary
• 19:1019:10, 5 March 2014 diff hist +418‎ Association ‎ →‎Example
• 19:0619:06, 5 March 2014 diff hist −39‎ MediaWiki:Sidebar ‎No edit summary
• 19:0519:05, 5 March 2014 diff hist +405‎ Beagle input ‎ →‎output
• 18:5918:59, 5 March 2014 diff hist −29‎ Beagle input ‎ →‎Example
• 18:5818:58, 5 March 2014 diff hist +139‎ Beagle input ‎No edit summary
• 18:5418:54, 5 March 2014 diff hist −45‎ SNP calling ‎No edit summary

26 February 2014

• 20:0420:04, 26 February 2014 diff hist +11‎ SNP calling ‎No edit summary
• 18:4318:43, 26 February 2014 diff hist −43‎ Allele Frequencies ‎ →‎.mafs
• 18:4318:43, 26 February 2014 diff hist −1‎ Allele Frequencies ‎ →‎.mafs
• 18:4318:43, 26 February 2014 diff hist +8‎ Allele Frequencies ‎ →‎.mafs
• 18:4018:40, 26 February 2014 diff hist +105‎ Allele Frequencies ‎ →‎.mafs
• 18:3718:37, 26 February 2014 diff hist −606‎ Allele Frequencies ‎ →‎.mafs
• 18:3618:36, 26 February 2014 diff hist +44‎ Allele Frequencies ‎ →‎Allele Frequency estimation
• 18:3618:36, 26 February 2014 diff hist +974‎ N SYKmaf ‎ Created page with "==ML estimator with known minor== First infer the Major and Minor allele and then use BFGS (-doMaf 1) optimazation or the EM algorithm (..."
• 18:3518:35, 26 February 2014 diff hist +41‎ Allele Frequencies ‎ →‎Allele Frequency estimation
• 18:3518:35, 26 February 2014 diff hist −985‎ Allele Frequencies ‎ →‎Theory
• 18:3418:34, 26 February 2014 diff hist +64‎ Allele Frequencies ‎No edit summary
• 18:3218:32, 26 February 2014 diff hist +11‎ User:Thorfinn ‎No edit summary
• 18:3218:32, 26 February 2014 diff hist +867‎ User:Thorfinn ‎ →‎Anders changes to version 583
• 18:1318:13, 26 February 2014 diff hist +330‎ User:Thorfinn ‎No edit summary
• 17:4717:47, 26 February 2014 diff hist +57‎ Allele Frequencies ‎ →‎Example
• 17:4617:46, 26 February 2014 diff hist −19‎ Allele Frequencies ‎No edit summary
• 17:4517:45, 26 February 2014 diff hist −420‎ Allele Frequencies ‎No edit summary
• 17:4417:44, 26 February 2014 diff hist +395‎ N PostFreq ‎ Created page with "==Estimator from genotype probabilities== If the genotype probabilities are known the frequencies can be estimated by summing up the posterior probabilities <math> p(G=g|D)</..." current
• 17:4417:44, 26 February 2014 diff hist −93‎ Allele Frequencies ‎No edit summary
• 17:4117:41, 26 February 2014 diff hist +5‎ Allele Frequencies ‎ →‎Example
• 17:3917:39, 26 February 2014 diff hist +824‎ Allele Frequencies ‎No edit summary
• 17:2517:25, 26 February 2014 diff hist +254‎ Error estimation ‎No edit summary
• 17:2317:23, 26 February 2014 diff hist −75‎ Error estimation ‎ →‎Theory
• 17:2117:21, 26 February 2014 diff hist +15‎ Error estimation ‎ →‎Example
• 17:1917:19, 26 February 2014 diff hist +34‎ Error estimation ‎ →‎Options
• 17:1817:18, 26 February 2014 diff hist +15‎ Error estimation ‎ →‎Options
• 17:1617:16, 26 February 2014 diff hist +314‎ Error estimation ‎ →‎Error estimation using an outgroup and an error free individual
• 17:1517:15, 26 February 2014 diff hist +2,063‎ N ErrorPerfect ‎ Created page with "==Method 2== The method was use in Orlando2013 and is described in details in supplementary 4.4 The estimated rates can roughly be intrepreted as relative error rates. T..." current
• 17:1317:13, 26 February 2014 diff hist +28‎ Error estimation ‎ →‎Error estimation using an outgroup and an error free individual
• 17:1317:13, 26 February 2014 diff hist −2,065‎ Error estimation ‎ →‎Method 2
• 17:1217:12, 26 February 2014 diff hist −13‎ ErrorSykMethod ‎No edit summary current
• 17:1217:12, 26 February 2014 diff hist +854‎ N ErrorSykMethod ‎ Created page with "==Method 1== The method is described in kim2011 and work by simultaneously estimating allele frequencies, genotype likelihoods and the error rates. The likelihood of t..."
• 17:1217:12, 26 February 2014 diff hist +69‎ Error estimation ‎ →‎Error estimation from polymorphic sites
• 17:1117:11, 26 February 2014 diff hist −856‎ Error estimation ‎ →‎Method 1
• 17:0817:08, 26 February 2014 diff hist +48‎ Error estimation ‎ →‎Output
• 17:0217:02, 26 February 2014 diff hist 0‎ Error estimation ‎No edit summary
• 16:1716:17, 26 February 2014 diff hist +1‎ Error estimation ‎No edit summary
• 16:1616:16, 26 February 2014 diff hist +11‎ Error estimation ‎ →‎Example
• 16:1216:12, 26 February 2014 diff hist +280‎ Error estimation ‎No edit summary
• 16:0716:07, 26 February 2014 diff hist +16‎ Error estimation ‎No edit summary
• 15:3315:33, 26 February 2014 diff hist 0‎ Major Minor ‎No edit summary
• 15:2915:29, 26 February 2014 diff hist +503‎ Major Minor ‎No edit summary
• 15:2315:23, 26 February 2014 diff hist +256‎ Major Minor ‎ →‎Details
• 15:1915:19, 26 February 2014 diff hist −29‎ Major Minor ‎ →‎From counts of data
• 15:1915:19, 26 February 2014 diff hist −1‎ Major Minor ‎ →‎From genotype likelihood data
• 15:1515:15, 26 February 2014 diff hist +1,283‎ N MajorMinor Method ‎ Created page with "==From Genotype Likelihoods== Assuming that the considered site is diallelic, we infer those two alleles using the genotype likelihoods. Let <math>\{M,m\}</math> denote the tw..." current
• 15:1515:15, 26 February 2014 diff hist +52‎ Major Minor ‎ →‎From genotype likelihood data
• 15:1415:14, 26 February 2014 diff hist −1,246‎ Major Minor ‎No edit summary
• 15:0315:03, 26 February 2014 diff hist −1,610‎ Genotype Likelihoods ‎ →‎Theory
• 15:0215:02, 26 February 2014 diff hist −10‎ Genotype Likelihoods ‎ →‎GATK genotype likelihoods
• 15:0115:01, 26 February 2014 diff hist −31‎ Genotype Likelihoods ‎ →‎Theory
• 14:5914:59, 26 February 2014 diff hist +111‎ Genotype Likelihoods ‎No edit summary
• 14:5714:57, 26 February 2014 diff hist −13‎ Genotype Likelihoods ‎ →‎SOAPsnp
• 14:5714:57, 26 February 2014 diff hist −87‎ Genotype Likelihoods ‎No edit summary
• 14:4514:45, 26 February 2014 diff hist −16‎ MediaWiki:Sidebar ‎No edit summary
• 14:4314:43, 26 February 2014 diff hist −14‎ Fasta ‎ →‎Options
• 14:4114:41, 26 February 2014 diff hist −149‎ Fasta ‎No edit summary
• 14:2114:21, 26 February 2014 diff hist +6‎ Fasta ‎No edit summary
• 14:1714:17, 26 February 2014 diff hist +19‎ Allele Counts ‎No edit summary
• 13:5913:59, 26 February 2014 diff hist +123‎ Association ‎No edit summary
• 13:5113:51, 26 February 2014 diff hist +1,357‎ Association ‎No edit summary
• 13:1913:19, 26 February 2014 diff hist +34‎ Abbababa ‎ →‎Options
• 13:1613:16, 26 February 2014 diff hist +73‎ User:Thorfinn ‎No edit summary
• 13:1513:15, 26 February 2014 diff hist +10‎ Thetas,Tajima,Neutrality tests ‎No edit summary
• 13:1413:14, 26 February 2014 diff hist +9‎ Filters ‎ →‎Filters for Bam files
• 13:1313:13, 26 February 2014 diff hist +33‎ Filters ‎ →‎Examples
• 12:1312:13, 26 February 2014 diff hist −4‎ Filters ‎ →‎Examples
• 12:1212:12, 26 February 2014 diff hist +6‎ Filters ‎ →‎Examples
• 12:1212:12, 26 February 2014 diff hist +435‎ Filters ‎ →‎Examples
• 12:0512:05, 26 February 2014 diff hist +21‎ Filters ‎ →‎Extra
• 12:0412:04, 26 February 2014 diff hist −1,846‎ Filters ‎No edit summary
• 11:4411:44, 26 February 2014 diff hist +65‎ Input ‎No edit summary
• 11:3211:32, 26 February 2014 diff hist +114‎ Quick Start ‎ →‎Examples
• 11:1811:18, 26 February 2014 diff hist −1‎ Quick Start ‎ →‎Examples
• 11:1711:17, 26 February 2014 diff hist +8‎ Quick Start ‎No edit summary
• 11:1611:16, 26 February 2014 diff hist −88‎ Quick Start ‎No edit summary
• 11:1311:13, 26 February 2014 diff hist −146‎ Quick Start ‎ →‎Download and prepare

7 February 2014

• 15:1615:16, 7 February 2014 diff hist +56‎ Abbababa ‎ →‎Output
• 15:1515:15, 7 February 2014 diff hist +95‎ Abbababa ‎ →‎Output
• 13:0013:00, 7 February 2014 diff hist −4‎ HWE and Inbreeding estimates ‎No edit summary
• 12:3012:30, 7 February 2014 diff hist −100‎ HWE and Inbreeding estimates ‎No edit summary

6 February 2014

• 09:4309:43, 6 February 2014 diff hist +93‎ User:Thorfinn ‎No edit summary

3 February 2014

• 16:2616:26, 3 February 2014 diff hist +59‎ User:Thorfinn ‎No edit summary
• 16:0216:02, 3 February 2014 diff hist +147‎ User:Thorfinn ‎No edit summary

30 January 2014

• 19:0619:06, 30 January 2014 diff hist +38‎ User:Thorfinn ‎No edit summary
• 18:1418:14, 30 January 2014 diff hist +76‎ User:Thorfinn ‎No edit summary
• 17:4217:42, 30 January 2014 diff hist −1‎ Fasta ‎No edit summary
• 17:4217:42, 30 January 2014 diff hist −1‎ Major Minor ‎No edit summary

3 January 2014

• 15:1315:13, 3 January 2014 diff hist +2‎ Error estimation ‎ →‎Method 1
• 15:1315:13, 3 January 2014 diff hist +260‎ Error estimation ‎ →‎Method 1
• 15:0815:08, 3 January 2014 diff hist +74‎ Error estimation ‎ →‎Method 1
• 15:0615:06, 3 January 2014 diff hist +381‎ Error estimation ‎ →‎Method 1
• 14:5414:54, 3 January 2014 diff hist +2‎ Error estimation ‎ →‎Method 1
• 14:5314:53, 3 January 2014 diff hist +124‎ Error estimation ‎ →‎Method 1
• 14:4814:48, 3 January 2014 diff hist +22‎ Error estimation ‎ →‎Method 2
• 14:4714:47, 3 January 2014 diff hist −201‎ Error estimation ‎ →‎Method 2
• 14:4114:41, 3 January 2014 diff hist +127‎ Error estimation ‎ →‎Method 2
• 14:3914:39, 3 January 2014 diff hist +179‎ Error estimation ‎ →‎Method 2
• 14:3214:32, 3 January 2014 diff hist +430‎ Error estimation ‎ →‎Method 2
• 14:1914:19, 3 January 2014 diff hist +22‎ Error estimation ‎ →‎Method 2
• 14:1614:16, 3 January 2014 diff hist +847‎ N Orlando2013 ‎ Created page with "Orlando, L, Ginolhac, A, Zhang, G, Froese, D, Albrechtsen, A, Stiller, M, Schubert, M, Cappellini, E, Petersen, B, Moltke, I, Johnson, PL, Fumagalli, M, Vilstrup, JT, Raghavan..."
• 14:1614:16, 3 January 2014 diff hist +144‎ Citing angsd ‎ →‎Methods
• 14:1214:12, 3 January 2014 diff hist −77‎ User:Albrecht ‎No edit summary
• 14:1214:12, 3 January 2014 diff hist −32‎ Abbababa ‎No edit summary
• 14:1114:11, 3 January 2014 diff hist +3‎ Abbababa ‎No edit summary
• 14:0814:08, 3 January 2014 diff hist +46‎ Abbababa ‎ →‎Brief Overview
• 13:1813:18, 3 January 2014 diff hist −10‎ Error estimation ‎No edit summary
• 13:1713:17, 3 January 2014 diff hist −10‎ Genotype Likelihoods ‎No edit summary
• 13:1613:16, 3 January 2014 diff hist −15‎ Depth ‎No edit summary current
• 13:1513:15, 3 January 2014 diff hist −14‎ Abbababa ‎No edit summary
• 13:1413:14, 3 January 2014 diff hist −10‎ SFS Estimation ‎No edit summary
• 12:5512:55, 3 January 2014 diff hist +8‎ Quick Start ‎ →‎Examples
• 12:5412:54, 3 January 2014 diff hist +1‎ Quick Start ‎ →‎Download and prepare
• 12:4512:45, 3 January 2014 diff hist +11‎ Quick Start ‎ →‎Download and prepare

16 December 2013

• 17:4617:46, 16 December 2013 diff hist +22‎ User:Thorfinn ‎No edit summary

7 December 2013

• 19:0219:02, 7 December 2013 diff hist +19‎ Major Minor ‎ →‎From Genotype Likelihoods

5 December 2013

• 16:4016:40, 5 December 2013 diff hist +32‎ Error estimation ‎No edit summary
• 16:3516:35, 5 December 2013 diff hist 0‎ Error estimation ‎No edit summary

4 December 2013

• 14:4014:40, 4 December 2013 diff hist +689‎ Allele Counts ‎ →‎Example
• 14:3214:32, 4 December 2013 diff hist +340‎ Allele Counts ‎ →‎Filtering
• 14:2714:27, 4 December 2013 diff hist +66‎ Allele Counts ‎ →‎Brief Overview
• 14:2414:24, 4 December 2013 diff hist +115‎ Abbababa ‎ →‎Options

2 December 2013

• 18:5518:55, 2 December 2013 diff hist +18‎ Abbababa ‎ →‎output
• 18:5518:55, 2 December 2013 diff hist +7‎ Abbababa ‎ →‎Method
• 18:5318:53, 2 December 2013 diff hist 0‎ N File:Tree.png ‎No edit summary current
• 18:5318:53, 2 December 2013 diff hist +28‎ Abbababa ‎No edit summary
• 18:4418:44, 2 December 2013 diff hist +55‎ MediaWiki:Sidebar ‎No edit summary
• 18:4118:41, 2 December 2013 diff hist −15‎ MediaWiki:Sidebar ‎No edit summary
• 18:4018:40, 2 December 2013 diff hist +22‎ MediaWiki:Sidebar ‎No edit summary
• 18:3618:36, 2 December 2013 diff hist +1‎ MediaWiki:Sidebar ‎No edit summary
• 18:3518:35, 2 December 2013 diff hist +56‎ MediaWiki:Sidebar ‎No edit summary
• 18:2818:28, 2 December 2013 diff hist −51‎ Abbababa ‎ →‎Example
• 18:2818:28, 2 December 2013 diff hist +6‎ Abbababa ‎ →‎output
• 18:2418:24, 2 December 2013 diff hist +35‎ Abbababa ‎ →‎output
• 18:2218:22, 2 December 2013 diff hist +1,555‎ Abbababa ‎No edit summary
• 18:1518:15, 2 December 2013 diff hist +79‎ Abbababa ‎ →‎Example
• 18:1318:13, 2 December 2013 diff hist +426‎ Abbababa ‎No edit summary
• 16:1416:14, 2 December 2013 diff hist +47‎ Abbababa ‎No edit summary
• 16:1216:12, 2 December 2013 diff hist +12‎ Abbababa ‎No edit summary
• 16:1116:11, 2 December 2013 diff hist −944‎ Abbababa ‎No edit summary
• 16:0616:06, 2 December 2013 diff hist +2,257‎ N Abbababa ‎ Created page with "Available from version 0.559+. performs the abbababa test also called the D-statistic. This tests for ancient admixture (or wrong tree topology) <classdiagram type="dir:LR">..."

27 November 2013

• 22:0622:06, 27 November 2013 diff hist −2‎ Fasta ‎No edit summary
• 22:0522:05, 27 November 2013 diff hist −2‎ Fasta ‎No edit summary
• 18:5018:50, 27 November 2013 diff hist +39‎ Fasta ‎No edit summary
• 18:4818:48, 27 November 2013 diff hist +31‎ Fasta ‎No edit summary
• 18:4718:47, 27 November 2013 diff hist +116‎ Fasta ‎No edit summary
• 18:4418:44, 27 November 2013 diff hist 0‎ Fasta ‎No edit summary
• 18:4418:44, 27 November 2013 diff hist +1‎ Fasta ‎ →‎Example
• 18:4318:43, 27 November 2013 diff hist −5,515‎ Fasta ‎No edit summary
• 18:3418:34, 27 November 2013 diff hist +6,504‎ N Fasta ‎ Created page with "This option create a fasta file from a sequencing data file. <classdiagram type="dir:LR"> [One bam file{bg:orange}]->[sequencing data|random base (-doFasta 1);consensus base..."
• 18:2418:24, 27 November 2013 diff hist +29‎ MediaWiki:Sidebar ‎No edit summary

28 June 2013

• 14:0014:00, 28 June 2013 diff hist +2‎ Association ‎ →‎Score statistic
• 13:5913:59, 28 June 2013 diff hist +104‎ Association ‎ →‎Score statistic

11 June 2013

• 12:3812:38, 11 June 2013 diff hist +66‎ Error estimation ‎ →‎Error estimation using an outgroup and an error free individual

22 March 2013

• 19:1219:12, 22 March 2013 diff hist +66‎ MediaWiki:Sidebar ‎No edit summary
• 19:1019:10, 22 March 2013 diff hist +130‎ MediaWiki:Sidebar ‎No edit summary
• 16:2716:27, 22 March 2013 diff hist −33‎ ANGSD ‎No edit summary

27 February 2013

• 12:1112:11, 27 February 2013 diff hist −72‎ Base quality ‎ →‎options
• 12:1012:10, 27 February 2013 diff hist −67‎ Error estimation ‎ →‎additional options
• 12:1012:10, 27 February 2013 diff hist −72‎ Allele Counts ‎ →‎options
• 12:1012:10, 27 February 2013 diff hist −72‎ Genotype Likelihoods ‎ →‎options
• 12:0812:08, 27 February 2013 diff hist −71‎ Genotype Likelihoods ‎ →‎options
• 12:0812:08, 27 February 2013 diff hist −72‎ Genotype Likelihoods ‎ →‎options

13 February 2013

• 11:5011:50, 13 February 2013 diff hist +278‎ Error estimation ‎ →‎example

12 February 2013

• 18:1218:12, 12 February 2013 diff hist −17‎ Error estimation ‎ →‎Error estimation using an outgroup and an error free individual
• 18:1218:12, 12 February 2013 diff hist +116‎ Error estimation ‎ →‎Error estimation using an outgroup and an error free individual
• 18:0618:06, 12 February 2013 diff hist +719‎ Error estimation ‎ →‎Error estimation using an outgroup and an error free individual
• 17:5317:53, 12 February 2013 diff hist −14‎ Error estimation method ‎No edit summary current
• 17:5217:52, 12 February 2013 diff hist +1,483‎ N Error estimation method ‎ Created page with " The estimated rates can roughly be intrepreted as relative error rates. That is excess of errors in your sample compare to the error in the perfect indviduals. The idea is th..."

29 January 2013

• 19:1719:17, 29 January 2013 diff hist +1‎ Depth ‎ →‎Output

17 January 2013

• 20:2320:23, 17 January 2013 diff hist +16‎ Input ‎ →‎arguments

14 January 2013

• 19:5819:58, 14 January 2013 diff hist 0‎ Association ‎ →‎Score statistic (prefix lrt*)

4 December 2012

• 19:1019:10, 4 December 2012 diff hist −1,035‎ Bugs ‎No edit summary
• 18:5818:58, 4 December 2012 diff hist +17‎ Bugs ‎No edit summary

23 October 2012

• 21:1721:17, 23 October 2012 diff hist 0‎ MediaWiki:Sidebar ‎No edit summary
• 21:1021:10, 23 October 2012 diff hist −2‎ MediaWiki:Sidebar ‎No edit summary
• 20:4420:44, 23 October 2012 diff hist −2,321‎ Change log ‎ →‎Version notes
• 20:3620:36, 23 October 2012 diff hist 0‎ Citing angsd ‎ →‎Maf estimation from counts of alleles
• 20:3620:36, 23 October 2012 diff hist +2‎ Citing angsd ‎ →‎Maf estimation from counts of alleles
• 19:0919:09, 23 October 2012 diff hist +29‎ MediaWiki:Sidebar ‎No edit summary
• 19:0819:08, 23 October 2012 diff hist +33‎ MediaWiki:Sidebar ‎No edit summary

16 October 2012

• 15:5515:55, 16 October 2012 diff hist 0‎ MediaWiki:Sidebar ‎No edit summary
• 15:5015:50, 16 October 2012 diff hist +4‎ Citing angsd ‎ →‎Maf estimation from counts of alleles
• 15:5015:50, 16 October 2012 diff hist −2‎ Citing angsd ‎ →‎Maf estimation from counts of alleles
• 15:4815:48, 16 October 2012 diff hist +7‎ MediaWiki:Sidebar ‎No edit summary
• 15:4415:44, 16 October 2012 diff hist −13‎ Error estimation ‎ →‎example
• 15:4115:41, 16 October 2012 diff hist −380‎ Installation ‎ →‎Misc folder

10 October 2012

• 21:0021:00, 10 October 2012 diff hist −29‎ Major Minor ‎ →‎From genotype likelihood data
• 21:0021:00, 10 October 2012 diff hist −1‎ Major Minor ‎ →‎From alignment data
• 20:5920:59, 10 October 2012 diff hist +17‎ Major Minor ‎ →‎From genotype probability data
• 20:1020:10, 10 October 2012 diff hist +9‎ MediaWiki:Sidebar ‎No edit summary
• 20:1020:10, 10 October 2012 diff hist +1‎ Genotype calling ‎ →‎example
• 20:0920:09, 10 October 2012 diff hist +1,248‎ Genotype calling ‎ →‎Genotype calling
• 18:3818:38, 10 October 2012 diff hist −143‎ Genotype calling ‎ →‎Genotype calling
• 16:4916:49, 10 October 2012 diff hist +63‎ Association ‎ →‎example
• 15:1815:18, 10 October 2012 diff hist +20‎ Association ‎ →‎example
• 15:1615:16, 10 October 2012 diff hist +40‎ Association ‎ →‎example
• 15:0215:02, 10 October 2012 diff hist +346‎ Association ‎ →‎Score statistic
• 15:0015:00, 10 October 2012 diff hist +143‎ Association ‎ →‎Case control association using allele frequencies
• 14:5014:50, 10 October 2012 diff hist −6‎ Association ‎No edit summary
• 14:5014:50, 10 October 2012 diff hist +95‎ Association ‎ →‎Case control association using allele frequencies
• 14:2414:24, 10 October 2012 diff hist +18‎ MediaWiki:Sidebar ‎No edit summary
• 14:2414:24, 10 October 2012 diff hist +9‎ MediaWiki:Sidebar ‎No edit summary
• 11:2411:24, 10 October 2012 diff hist +228‎ Input ‎ →‎genotype probability files

28 September 2012

• 16:2616:26, 28 September 2012 diff hist +1‎ Input ‎ →‎optional arguments

24 September 2012

• 17:3117:31, 24 September 2012 diff hist −16‎ Installation ‎ →‎Download
• 15:2915:29, 24 September 2012 diff hist −53‎ Filters ‎ →‎Selected Sites
• 13:5513:55, 24 September 2012 diff hist +123‎ Citing angsd ‎ →‎Methods
• 13:3513:35, 24 September 2012 diff hist +260‎ N Gatk ‎ Created page with "McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce ..."
• 13:3413:34, 24 September 2012 diff hist +80‎ Citing angsd ‎No edit summary
• 13:3213:32, 24 September 2012 diff hist +175‎ N SoapSNP ‎ Created page with "Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. SNP detection for massively parallel whole-genome resequencing. Genome Res. 2009 Jun;19(6):1124-32. Epub 2009 May 6." current
• 13:2813:28, 24 September 2012 diff hist −7‎ Citing angsd ‎No edit summary
• 13:2813:28, 24 September 2012 diff hist −179‎ Skotte ‎ Blanked the page current
• 13:2713:27, 24 September 2012 diff hist +179‎ N Skotte2012 ‎ Created page with "Line Skotte, Thorfinn Sand Korneliussen, Anders Albrechtsen. Association testing for next-generation sequencing data using score statistics. Genet Epidemiol. 2012 Jul;36(5):43..."
• 13:2513:25, 24 September 2012 diff hist −221‎ SuYeon ‎ Redirected page to Kim2011 current
• 13:2513:25, 24 September 2012 diff hist +242‎ N Kim2011 ‎ Created page with "Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witte D, et al., 2011. Estimation of allele frequency and association mappin..."
• 13:0713:07, 24 September 2012 diff hist +26‎ Filters ‎No edit summary
• 13:0613:06, 24 September 2012 diff hist +24‎ Filters ‎No edit summary
• 13:0513:05, 24 September 2012 diff hist +72‎ Filters ‎No edit summary

21 September 2012

• 15:4715:47, 21 September 2012 diff hist +376‎ N Citing angsd ‎ Created page with "Currently there is not publication for angsd. However, many of the method implimented here are published. **Methods** allele estimation from genotype likelihoods ;- doMaf ..."
• 15:4315:43, 21 September 2012 diff hist +29‎ MediaWiki:Sidebar ‎No edit summary
• 15:2715:27, 21 September 2012 diff hist +1,787‎ SNP calling ‎No edit summary
• 15:1015:10, 21 September 2012 diff hist −36‎ MediaWiki:Sidebar ‎No edit summary

20 September 2012

• 15:5015:50, 20 September 2012 diff hist +392‎ Error estimation ‎No edit summary

19 September 2012

• 18:1518:15, 19 September 2012 diff hist +281‎ Genotype Likelihoods ‎ →‎output genotype likelihoods
• 18:0318:03, 19 September 2012 diff hist +2,006‎ Genotype Likelihoods ‎ →‎output genotype likelihoods
• 18:0018:00, 19 September 2012 diff hist +1‎ Genotype Likelihoods ‎No edit summary
• 17:4817:48, 19 September 2012 diff hist +915‎ Genotype Likelihoods ‎No edit summary
• 17:3517:35, 19 September 2012 diff hist +36‎ Genotype Likelihoods ‎ →‎Genotype likelihoods from alignments
• 17:2317:23, 19 September 2012 diff hist +296‎ Base quality ‎No edit summary
• 17:2217:22, 19 September 2012 diff hist +15‎ Base quality ‎ →‎Example
• 17:2117:21, 19 September 2012 diff hist −21‎ Base quality ‎No edit summary
• 17:2017:20, 19 September 2012 diff hist +353‎ Base quality ‎No edit summary
• 17:1117:11, 19 September 2012 diff hist +196‎ N Base quality ‎ Created page with "=Base quality counts= Counts the number of bases for each quality. ==Example== Print the individuals depth from bam files <pre> ./angsd -out out -doCounts 1 -doQsDist 1 -ba..."
• 17:0317:03, 19 September 2012 diff hist +42‎ Allele Counts ‎ →‎options
• 16:5816:58, 19 September 2012 diff hist +44‎ MediaWiki:Sidebar ‎No edit summary
• 16:5616:56, 19 September 2012 diff hist +106‎ Allele Counts ‎ →‎options
• 16:5316:53, 19 September 2012 diff hist +251‎ Allele Counts ‎No edit summary

17 September 2012

• 16:1516:15, 17 September 2012 diff hist +6‎ Genotype Likelihoods ‎ →‎soapSNP
• 16:0416:04, 17 September 2012 diff hist −34‎ Genotype Likelihoods ‎ →‎Genotype likelihoods from alignments

16 July 2012

• 18:3918:39, 16 July 2012 diff hist +184‎ Genotype Likelihoods ‎ →‎Samtools
• 18:1618:16, 16 July 2012 diff hist −70‎ Genotype Likelihoods ‎ →‎soapSNP

22 June 2012

• 16:0016:00, 22 June 2012 diff hist +64‎ Genotype Likelihoods ‎ →‎Genotype likelihoods from alignments

21 June 2012

• 16:5416:54, 21 June 2012 diff hist +97‎ Genotype Likelihoods ‎ →‎Genotype likelihoods from alignments
• 11:4511:45, 21 June 2012 diff hist +30‎ Association ‎ →‎Score statistic
• 11:4211:42, 21 June 2012 diff hist −97‎ Association ‎ →‎Association study
• 11:3411:34, 21 June 2012 diff hist +1,043‎ Association ‎ →‎Association
• 10:2310:23, 21 June 2012 diff hist +242‎ Beagle input ‎ →‎output
• 10:2110:21, 21 June 2012 diff hist +1,687‎ N Beagle input ‎ Created page with "Beagle haplotype imputation and be performed directly on genotype likelhoods. To generate beagle input file use ; -doGlf 2 In order to make this file the major and minor all..."
• 10:1210:12, 21 June 2012 diff hist +32‎ Association ‎ →‎Association
• 10:1110:11, 21 June 2012 diff hist +271‎ N Example of a covariate file ‎ Created page with "1 0 0 1 <br> 1 0.1 0 0 <br> 2 0 1 0 <br> 2 0 1 0 <br> 2 0.1 0 1 <br> 1 0 0 1 <br> 1 0.3 0 0 <br> 2 0 0 0 <br> 1 0 0 0 <br> 2 0.2 0 1 <br> 1 0 1 0 <br> 1 0 0 0 <br> 1 0.1 0 0 <..." current
• 10:1110:11, 21 June 2012 diff hist −1‎ Association ‎ →‎Score statistic
• 10:1010:10, 21 June 2012 diff hist +271‎ N Example of a covariance file ‎ Created page with "1 0 0 1 <br> 1 0.1 0 0 <br> 2 0 1 0 <br> 2 0 1 0 <br> 2 0.1 0 1 <br> 1 0 0 1 <br> 1 0.3 0 0 <br> 2 0 0 0 <br> 1 0 0 0 <br> 2 0.2 0 1 <br> 1 0 1 0 <br> 1 0 0 0 <br> 1 0.1 0 0 <..." current
• 10:1010:10, 21 June 2012 diff hist +364‎ N Example of a quantitative phenotype file ‎ Created page with "-999<br> 2.06164722761138<br> -0.091935218675602<br> -0.287527686061831<br> -999<br> -999<br> -1.20996664036026<br> 0.0188541092307412<br> -2.1122713873334<br> -999<br> -1.329..." current
• 10:0910:09, 21 June 2012 diff hist +98‎ N Example of cases control phenotype file ‎ Created page with "1<br> 0<br> 0<br> 0<br> 1<br> 1<br> 1<br> 1<br> 0<br> -999<br> 1<br> 0<br> 0<br> 0<br> 0<br> 1<br>" current

19 June 2012

• 15:2115:21, 19 June 2012 diff hist +66‎ Input ‎ →‎optional arguments
• 13:4313:43, 19 June 2012 diff hist +1‎ ANGSD ‎ →‎Overview of input and intermediary data
• 13:3813:38, 19 June 2012 diff hist +30‎ ANGSD ‎ →‎Synopsis
• 11:0311:03, 19 June 2012 diff hist +10‎ MediaWiki:Sidebar ‎No edit summary
• 10:5410:54, 19 June 2012 diff hist +200‎ Genotype Likelihoods ‎ →‎Genotype likelihoods from alignments

18 June 2012

• 20:4720:47, 18 June 2012 diff hist 0‎ Genotype Likelihoods ‎ →‎Genotype likelihoods from alignments
• 20:0520:05, 18 June 2012 diff hist +178‎ Genotype Likelihoods ‎No edit summary
• 19:5519:55, 18 June 2012 diff hist −3‎ MediaWiki:Sidebar ‎No edit summary
• 19:5319:53, 18 June 2012 diff hist +1,262‎ Allele Counts ‎ →‎dumping counts
• 19:3919:39, 18 June 2012 diff hist −1‎ Allele Frequencies ‎ →‎Allele Frequency estimation
• 19:3519:35, 18 June 2012 diff hist +240‎ ANGSD ‎ →‎Analysis from genotype probabilities
• 19:0619:06, 18 June 2012 diff hist +14‎ Input ‎ →‎glfv3
• 19:0419:04, 18 June 2012 diff hist +54‎ ANGSD ‎ →‎About
• 19:0319:03, 18 June 2012 diff hist −463‎ ANGSD ‎ →‎Commands
• 18:2318:23, 18 June 2012 diff hist −10‎ Allele Frequencies ‎No edit summary
• 18:2118:21, 18 June 2012 diff hist −12‎ Input ‎No edit summary
• 18:1118:11, 18 June 2012 diff hist −79‎ ANGSD ‎ →‎Wish list
• 18:0818:08, 18 June 2012 diff hist +86‎ Change log ‎ →‎Version notes
• 18:0818:08, 18 June 2012 diff hist −649‎ ANGSD ‎ →‎Possible Bugs
• 18:0718:07, 18 June 2012 diff hist −1,934‎ ANGSD ‎ →‎Version notes
• 18:0718:07, 18 June 2012 diff hist +1,932‎ N Change log ‎ Created page with "=Version notes= * 0.16 Is now bundled with SAMtools-0.1.17 and the mpileup (and friends) command be used for passing data to dirty. * 0.17 added extra options -minInd and -min..."
• 18:0618:06, 18 June 2012 diff hist +26‎ MediaWiki:Sidebar ‎No edit summary
• 18:0618:06, 18 June 2012 diff hist +85‎ ANGSD ‎ →‎Possible Bugs
• 18:0518:05, 18 June 2012 diff hist −185‎ ANGSD ‎ →‎Example for getting the depths with bamfiles
• 18:0418:04, 18 June 2012 diff hist −322‎ ANGSD ‎ →‎sfstools
• 18:0418:04, 18 June 2012 diff hist −1,530‎ ANGSD ‎ →‎Run Examples
• 18:0418:04, 18 June 2012 diff hist +1,528‎ N Misc example ‎ Created page with "=Run Examples= ==Using glfv3== <code lang="sh"> ../dirty -samglf ceu.glf.list -outfiles test.glf -doMaf 2 -fai numSort.Fai -nLines 50000 -chunkSize 500 -nThreads 16 </code..."
• 18:0418:04, 18 June 2012 diff hist +36‎ MediaWiki:Sidebar ‎No edit summary
• 18:0318:03, 18 June 2012 diff hist −708‎ ANGSD ‎ →‎All options
• 17:3417:34, 18 June 2012 diff hist −97‎ ANGSD ‎ →‎Association study
• 17:2917:29, 18 June 2012 diff hist +97‎ Association ‎No edit summary
• 17:2417:24, 18 June 2012 diff hist −726‎ ANGSD ‎ →‎Input sequencing data
• 17:2417:24, 18 June 2012 diff hist +447‎ Input ‎ →‎genotype likelihood files
• 17:2217:22, 18 June 2012 diff hist −821‎ ANGSD ‎ →‎Output data
• 17:2217:22, 18 June 2012 diff hist −973‎ ANGSD ‎ →‎Association
• 16:3916:39, 18 June 2012 diff hist +983‎ Association ‎No edit summary
• 16:2916:29, 18 June 2012 diff hist +822‎ Allele Frequencies ‎ →‎Allele Frequency estimation
• 16:2716:27, 18 June 2012 diff hist −10‎ ANGSD ‎ →‎Methods
• 16:2716:27, 18 June 2012 diff hist −74‎ ANGSD ‎ →‎HWE and Inbreeding estimates
• 16:2716:27, 18 June 2012 diff hist +3,624‎ N Inbreed ‎ Created page with "Definition <math> \begin{align} p(AA)&=P_A^2+p_Ap_aF \\ p(Aa)&=2P_Ap_a-2p_Ap_aF \end{align} </math> ;n: total number of individuals ;X: all sequencing data ;f: allele frequ..." current
• 16:2616:26, 18 June 2012 diff hist +72‎ N HWE and Inbreeding estimates ‎ Created page with "==HWE and Inbreeding estimates== For method details see here"
• 16:2616:26, 18 June 2012 diff hist −21‎ ANGSD ‎ →‎Heterozygosity
• 16:2616:26, 18 June 2012 diff hist −1,603‎ ANGSD ‎ →‎Full example for simulating nextgen data and estimating SFS (somewhat deprecated should use sfstools now)
• 16:2516:25, 18 June 2012 diff hist +1,603‎ SFS Estimation ‎No edit summary
• 16:2516:25, 18 June 2012 diff hist −686‎ ANGSD ‎ →‎Download and Installation
• 16:2416:24, 18 June 2012 diff hist +380‎ Installation ‎No edit summary
• 16:2116:21, 18 June 2012 diff hist −2,753‎ ANGSD ‎ →‎Association
• 16:2116:21, 18 June 2012 diff hist +2,751‎ N Association ‎ Created page with "==Association== Association can be performed using two approaches. One based on testing differences in allele frequencies between cases and control while the other is based o..."
• 16:2116:21, 18 June 2012 diff hist −97‎ MediaWiki:Sidebar ‎No edit summary
• 16:2016:20, 18 June 2012 diff hist +97‎ MediaWiki:Sidebar ‎No edit summary
• 16:1916:19, 18 June 2012 diff hist +29‎ N Covariance matrix for PCA ‎ Created page with "==Covariance matrix for PCA==" current
• 16:1916:19, 18 June 2012 diff hist −31‎ ANGSD ‎ →‎Covariance matrix for PCA
• 16:1816:18, 18 June 2012 diff hist +745‎ N SNP calling ‎ Created page with "==SNP Calling== ===Likelihood ratio test=== supply -doSNP 1 Then the MAF estimate(s) given by -doMaf INT, will be used for a like ratio test <pre> chromo position ma..."
• 16:1816:18, 18 June 2012 diff hist −747‎ ANGSD ‎ →‎SNP Calling
• 16:1816:18, 18 June 2012 diff hist +27‎ MediaWiki:Sidebar ‎No edit summary
• 16:1816:18, 18 June 2012 diff hist +125‎ N Genotype Likelihoods ‎ Created page with "==Genotype likelihoods from alignments== ===Kim et al.=== Citation Citation ===Samtools=== ===GATK==="
• 16:1716:17, 18 June 2012 diff hist −127‎ ANGSD ‎ →‎Genotype likelihoods from alignments
• 16:1716:17, 18 June 2012 diff hist −780‎ ANGSD ‎ →‎Genotype calling
• 16:1716:17, 18 June 2012 diff hist +778‎ N Genotype calling ‎ Created page with "==Genotype calling== output file .geno -doGeno 1, print out major minor -doGeno 2, print the called genotype under HWE (suyeon maf prior method) -doGeno 4, print out the g..."
• 16:1716:17, 18 June 2012 diff hist +17‎ MediaWiki:Sidebar ‎No edit summary
• 16:1616:16, 18 June 2012 diff hist +20‎ MediaWiki:Sidebar ‎No edit summary
• 16:1516:15, 18 June 2012 diff hist +2‎ MediaWiki:Sidebar ‎No edit summary
• 16:1516:15, 18 June 2012 diff hist −238‎ ANGSD ‎ →‎dumping counts
• 16:1516:15, 18 June 2012 diff hist +236‎ N Allele Counts ‎ Created page with "==dumping counts== -dumpCounts 1, print overall depth in the .pos file -dumpCounts 2, 1) plus .counts with overall sample depth, each line nInd long -dumpCounts 3,..."
• 16:1416:14, 18 June 2012 diff hist +44‎ MediaWiki:Sidebar ‎No edit summary
• 16:1416:14, 18 June 2012 diff hist −86‎ ANGSD ‎ →‎Error estimation
• 16:1416:14, 18 June 2012 diff hist +84‎ N Error estimation ‎ Created page with "==Error estimation== ===Kim et al.=== Citation ===Using an outgroup==="
• 16:1316:13, 18 June 2012 diff hist −336‎ ANGSD ‎ →‎realSFS
• 16:1316:13, 18 June 2012 diff hist +334‎ N SFS Estimation ‎ Created page with "==realSFS== From version 0.20 we can now estimate the joint likelihood of being in frequency j. From version 0.24 the tajima is being estimated -realSFS 1 an sfs file will ..."
• 15:5515:55, 18 June 2012 diff hist +2‎ Allele Frequencies ‎ →‎Example
• 15:5515:55, 18 June 2012 diff hist +174‎ Allele Frequencies ‎ →‎Estimator from genotype probabilities
• 15:5315:53, 18 June 2012 diff hist +397‎ Allele Frequencies ‎ →‎Allele frequencies from genotype likelihoods
• 14:4414:44, 18 June 2012 diff hist +91‎ Allele Frequencies ‎ →‎Estimator from sequencing data
• 13:2713:27, 18 June 2012 diff hist +1‎ Allele Frequencies ‎ →‎ML estimator with known minor
• 13:2713:27, 18 June 2012 diff hist +2‎ Allele Frequencies ‎ →‎Allele Frequency estimation
• 13:2613:26, 18 June 2012 diff hist +305‎ Allele Frequencies ‎No edit summary
• 12:1512:15, 18 June 2012 diff hist +1,576‎ Allele Frequencies ‎No edit summary

15 June 2012

• 11:1411:14, 15 June 2012 diff hist +242‎ N SuYeon ‎ Created page with "Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witte D, et al., 2011. Estimation of allele frequency and association mappin..."
• 11:1411:14, 15 June 2012 diff hist +4‎ Allele Frequencies ‎No edit summary
• 11:1311:13, 15 June 2012 diff hist +229‎ Allele Frequencies ‎No edit summary

14 June 2012

• 22:0222:02, 14 June 2012 diff hist +240‎ N Allele Frequencies ‎ Created page with "==Allele Frequency estimation== -doMaf INT INT=1 bfgs known minor INT=2 EM known minor INT=4 BFGS unknown minor INT=8 EM unknown minor ===Phat estimator=== ===ML est..."
• 21:5921:59, 14 June 2012 diff hist −242‎ ANGSD ‎ →‎Allele Frequency estimation
• 21:5921:59, 14 June 2012 diff hist −460‎ ANGSD ‎ →‎Inferring Major and Minor alleles
• 21:4121:41, 14 June 2012 diff hist +1,183‎ N Majorminor ‎ Created page with "Assuming that the considered site is diallelic, we infer those two alleles using the genotype likelihoods. Let <math>\{M,m\}</math> denote the two possible alleles at the dial..." current
• 21:4121:41, 14 June 2012 diff hist +179‎ N Skotte ‎ Created page with "Line Skotte, Thorfinn Sand Korneliussen, Anders Albrechtsen. Association testing for next-generation sequencing data using score statistics. Genet Epidemiol. 2012 Jul;36(5):43..."
• 21:4021:40, 14 June 2012 diff hist +256‎ N Li2010 ‎ Created page with "Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, et al., 2010. Resequencing of 200 human exomes identifies a..." current
• 21:3921:39, 14 June 2012 diff hist +1,015‎ Major Minor ‎No edit summary
• 20:2320:23, 14 June 2012 diff hist −3‎ Input ‎ →‎optional arguments
• 20:2320:23, 14 June 2012 diff hist +179‎ Input ‎ →‎optional arguments
• 20:2120:21, 14 June 2012 diff hist +181‎ Input ‎ →‎obtional arguments
• 19:4519:45, 14 June 2012 diff hist +569‎ Input ‎ →‎bam files
• 19:2119:21, 14 June 2012 diff hist −3‎ Input ‎ →‎options
• 19:2119:21, 14 June 2012 diff hist −6‎ Input ‎ →‎Mapped sequence file
• 19:2119:21, 14 June 2012 diff hist +830‎ Input ‎No edit summary
• 19:1619:16, 14 June 2012 diff hist −17‎ Input ‎ →‎Mapped sequence file
• 19:0219:02, 14 June 2012 diff hist −4‎ Input ‎ →‎example
• 18:5718:57, 14 June 2012 diff hist +285‎ N Installation ‎ Created page with "=Download= The source code is avaible as a tarball and be download here [http://popgen.dk/software/download/angsd/angsd0.3.tar.gz] =Install= Unpack the tarball ===Unix=== Th..."

11 June 2012

• 17:0917:09, 11 June 2012 diff hist +1‎ Input ‎ →‎example
• 16:5216:52, 11 June 2012 diff hist +988‎ Input ‎ →‎beagle format
• 12:2912:29, 11 June 2012 diff hist +26‎ MediaWiki:Sidebar ‎No edit summary
• 12:2812:28, 11 June 2012 diff hist −120‎ MediaWiki:Sidebar ‎No edit summary
• 12:2312:23, 11 June 2012 diff hist −10‎ MediaWiki:Sidebar ‎No edit summary
• 12:2312:23, 11 June 2012 diff hist +11‎ MediaWiki:Sidebar ‎No edit summary
• 12:2312:23, 11 June 2012 diff hist −16‎ MediaWiki:Sidebar ‎No edit summary
• 12:2212:22, 11 June 2012 diff hist +257‎ N Input ‎ Created page with "ANSGD currently supports various mapped data, genotype likelihood formats and imputed genotype probability files =Mapped sequence file= ==bam files== ==soap files== =geno..."
• 12:1912:19, 11 June 2012 diff hist −14‎ ANGSD ‎ →‎Input data
• 12:1612:16, 11 June 2012 diff hist −633‎ ANGSD ‎No edit summary
• 12:1412:14, 11 June 2012 diff hist +16‎ ANGSD ‎No edit summary
• 11:5911:59, 11 June 2012 diff hist +161‎ ANGSD ‎ →‎About
• 11:5511:55, 11 June 2012 diff hist +30‎ ANGSD ‎ →‎overview
• 11:5311:53, 11 June 2012 diff hist +246‎ ANGSD ‎ →‎About
• 11:5011:50, 11 June 2012 diff hist +17‎ ANGSD ‎ →‎About
• 11:4811:48, 11 June 2012 diff hist +28‎ ANGSD ‎ →‎About
• 11:4711:47, 11 June 2012 diff hist +30‎ MediaWiki:Sitenotice ‎No edit summary
• 11:4511:45, 11 June 2012 diff hist 0‎ File:Banner.png ‎ Albrecht uploaded a new version of "File:Banner.png" current
• 11:4211:42, 11 June 2012 diff hist −29‎ MediaWiki:Sitenotice ‎No edit summary
• 11:4111:41, 11 June 2012 diff hist +28‎ MediaWiki:Sitenotice ‎No edit summary
• 11:4011:40, 11 June 2012 diff hist 0‎ File:Banner.png ‎ Albrecht uploaded a new version of "File:Banner.png"
• 11:3311:33, 11 June 2012 diff hist −27‎ ANGSD ‎No edit summary
• 11:3311:33, 11 June 2012 diff hist 0‎ N File:Banner.png ‎No edit summary
• 11:3211:32, 11 June 2012 diff hist 0‎ MediaWiki:Sitenotice ‎No edit summary
• 11:3211:32, 11 June 2012 diff hist +21‎ N MediaWiki:Sitenotice ‎ Created page with " Image:banner.gif"
• 11:3111:31, 11 June 2012 diff hist +29‎ ANGSD ‎No edit summary

29 May 2012

• 23:0323:03, 29 May 2012 diff hist −127‎ ANGSD ‎ →‎overview
• 23:0323:03, 29 May 2012 diff hist +6‎ ANGSD ‎ →‎About
• 23:0123:01, 29 May 2012 diff hist +330‎ ANGSD ‎ →‎overview
• 22:2422:24, 29 May 2012 diff hist −49‎ ANGSD ‎ →‎genotype probabilities
• 22:2422:24, 29 May 2012 diff hist −89‎ ANGSD ‎ →‎genotype likelihoods
• 22:2322:23, 29 May 2012 diff hist −52‎ ANGSD ‎ →‎sequencing data
• 21:4721:47, 29 May 2012 diff hist +587‎ N Temp ‎ Created page with "<classdiagram> [sequence data]->[genotype;likelihoods] [bam files{bg:orange}]->[sequence data] [SOAP files{bg:orange}]->[sequence data] [sequence data]->[phat estimates;er..." current
• 21:4121:41, 29 May 2012 diff hist +233‎ ANGSD ‎ →‎genotype probabilities
• 21:3821:38, 29 May 2012 diff hist −21‎ ANGSD ‎ →‎About
• 21:3721:37, 29 May 2012 diff hist +344‎ ANGSD ‎ →‎genotype likelihoods
• 21:2921:29, 29 May 2012 diff hist +223‎ ANGSD ‎ →‎sequencing data
• 21:1721:17, 29 May 2012 diff hist +180‎ ANGSD ‎ →‎About
• 21:1721:17, 29 May 2012 diff hist +35‎ ANGSD ‎No edit summary
• 20:2420:24, 29 May 2012 diff hist 0‎ ANGSD ‎ →‎about
• 20:2420:24, 29 May 2012 diff hist −422‎ ANGSD ‎No edit summary
• 20:2220:22, 29 May 2012 diff hist +19‎ N Main Page ‎ Albrecht moved page Main Page to ANGSD current
• 20:2220:22, 29 May 2012 diff hist 0‎ m ANGSD ‎ Albrecht moved page Main Page to ANGSD
• 20:1620:16, 29 May 2012 diff hist +29‎ ANGSD ‎No edit summary
• 20:1020:10, 29 May 2012 diff hist 0‎ N File:AngsdLogo.png ‎No edit summary current
• 18:2018:20, 29 May 2012 diff hist +26‎ ANGSD ‎No edit summary
• 17:5517:55, 29 May 2012 diff hist +4‎ MediaWiki:Mainpage ‎No edit summary current
• 17:5417:54, 29 May 2012 diff hist +5‎ N MediaWiki:Mainpage ‎ Created page with "ANGSD"
• 17:4817:48, 29 May 2012 diff hist −399‎ MediaWiki:Sidebar ‎No edit summary
• 17:4517:45, 29 May 2012 diff hist −288‎ MediaWiki:Sidebar ‎No edit summary
• 17:4317:43, 29 May 2012 diff hist +1,617‎ N MediaWiki:Sidebar ‎ Created page with "* Pages ** http://130.225.210.106/dirtywiki/index.php/Main_Page#Download|dirty ** http://130.225.210.106/dirtywiki/index.php/Main_Page#Installation|Installation ** http://130...."
• 17:4217:42, 29 May 2012 diff hist +16,749‎ ANGSD ‎No edit summary
• 17:3717:37, 29 May 2012 diff hist −34‎ ANGSD ‎No edit summary