ANGSD: Analysis of next generation Sequencing Data
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User contributions for Thorfinn
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16 July 2013
- 17:4917:49, 16 July 2013 diff hist +24 MediaWiki:Sidebar No edit summary
- 17:4817:48, 16 July 2013 diff hist +7 NGSadmix No edit summary
- 17:4717:47, 16 July 2013 diff hist −4 NGSadmix No edit summary
- 17:4717:47, 16 July 2013 diff hist −1 NGSadmix No edit summary
- 17:4617:46, 16 July 2013 diff hist +19 NGSadmix No edit summary
- 17:4517:45, 16 July 2013 diff hist +2 NGSadmix No edit summary
- 17:4517:45, 16 July 2013 diff hist +62 N NGSadmix Created page with "NGSadmix has it's very own webpage. [wwww.popgen.dk/software]"
4 July 2013
- 14:1414:14, 4 July 2013 diff hist +34 Bugs →Bugs
2 July 2013
- 13:5913:59, 2 July 2013 diff hist +97 HWE and Inbreeding estimates →HWE and Inbreeding estimates
30 June 2013
- 17:3017:30, 30 June 2013 diff hist −20 Genotype likelihoods from alignments new →Brief Overview
- 17:3017:30, 30 June 2013 diff hist +485 Genotype likelihoods from alignments new No edit summary
- 17:2417:24, 30 June 2013 diff hist 0 Genotype likelihoods from alignments new No edit summary
- 17:2417:24, 30 June 2013 diff hist +3 Genotype likelihoods from alignments new No edit summary
- 17:2417:24, 30 June 2013 diff hist +193 Genotype likelihoods from alignments new No edit summary
- 17:1617:16, 30 June 2013 diff hist +4,458 N Genotype likelihoods from alignments new Created page with "=Genotype likelihoods from alignments= <classdiagram> // [input|bam files;SOAP files{bg:orange}]->[sequence data] [sequence data]->[genotype likelihoods|SAMtools;GATK;SOAPsnp..."
- 17:1517:15, 30 June 2013 diff hist −79 ANGSD No edit summary
29 June 2013
- 12:0212:02, 29 June 2013 diff hist +70 Association →Output
- 11:5811:58, 29 June 2013 diff hist −1 Association →Output
- 11:5811:58, 29 June 2013 diff hist 0 Association →Output
- 11:5811:58, 29 June 2013 diff hist +6 Association →Output
- 11:5011:50, 29 June 2013 diff hist +8 Association →Citations
- 11:4911:49, 29 June 2013 diff hist +52 Association →Citations
- 11:4611:46, 29 June 2013 diff hist +12 Association No edit summary
- 11:4311:43, 29 June 2013 diff hist +154 Gatk No edit summary current
- 11:4211:42, 29 June 2013 diff hist +395 Gatk No edit summary
- 11:4011:40, 29 June 2013 diff hist +1 Citing angsd No edit summary
- 11:3811:38, 29 June 2013 diff hist +6 Li2011 No edit summary current
- 11:3811:38, 29 June 2013 diff hist 0 Citing angsd →Genotype likelihoods
- 11:3711:37, 29 June 2013 diff hist +587 N Li2011 Created page with "A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, 27, 21:298..."
- 11:3111:31, 29 June 2013 diff hist +337 Nielsen2012 No edit summary current
- 11:2711:27, 29 June 2013 diff hist 0 Skotte2012 No edit summary current
- 11:1111:11, 29 June 2013 diff hist 0 Association →Output
- 11:1111:11, 29 June 2013 diff hist −62 Association →Output
- 11:0611:06, 29 June 2013 diff hist +98 Association →Output
- 11:0611:06, 29 June 2013 diff hist +41 N Maf Redirected page to Allele Frequency estimation current
- 11:0111:01, 29 June 2013 diff hist +1 Association →Output
- 11:0111:01, 29 June 2013 diff hist +14 Association →Output
- 11:0011:00, 29 June 2013 diff hist +93 Association →Output
- 10:5710:57, 29 June 2013 diff hist +47 N MajorMinor Redirected page to Inferring Major and Minor alleles current
- 10:5310:53, 29 June 2013 diff hist −7 Association →Output
- 10:4710:47, 29 June 2013 diff hist −17 Association →Output
- 10:3810:38, 29 June 2013 diff hist −37 Association →Output
- 10:3710:37, 29 June 2013 diff hist +26 Association →Output
- 10:3610:36, 29 June 2013 diff hist +14 Association →Output
- 10:3410:34, 29 June 2013 diff hist +3 Association →Output
- 10:3410:34, 29 June 2013 diff hist +64 Association →Output
- 10:3310:33, 29 June 2013 diff hist +3 Association →Output
- 10:3210:32, 29 June 2013 diff hist +105 Association →Output
- 10:2910:29, 29 June 2013 diff hist +20 Association →Output
- 10:2710:27, 29 June 2013 diff hist +42 Association →Output
- 10:2510:25, 29 June 2013 diff hist +1 Association →Output
- 10:2510:25, 29 June 2013 diff hist 0 Association →Output
- 10:2410:24, 29 June 2013 diff hist +85 Association →Output
- 10:2210:22, 29 June 2013 diff hist +42 Association →Output
- 10:2010:20, 29 June 2013 diff hist −2 Association →Output
- 10:2010:20, 29 June 2013 diff hist +96 Association →Output
- 10:1910:19, 29 June 2013 diff hist −20 Association →Output
- 10:1910:19, 29 June 2013 diff hist −27 Association →Output
- 10:0810:08, 29 June 2013 diff hist +10 Association →Dependency Chain
- 10:0810:08, 29 June 2013 diff hist 0 Association →output
- 10:0610:06, 29 June 2013 diff hist +1 Association No edit summary
- 10:0510:05, 29 June 2013 diff hist +17 Association No edit summary
- 10:0210:02, 29 June 2013 diff hist +602 Association No edit summary
28 June 2013
- 17:3017:30, 28 June 2013 diff hist −1 Association →Score statistic
- 17:2917:29, 28 June 2013 diff hist −1 Association →Score statistic
- 17:2817:28, 28 June 2013 diff hist −4 Association →Score statistic
- 17:2817:28, 28 June 2013 diff hist +4 Association →Case control association using allele frequencies
- 17:2717:27, 28 June 2013 diff hist +4 Association →Score statistic
- 17:2717:27, 28 June 2013 diff hist +4 Association →Score statistic
- 17:2717:27, 28 June 2013 diff hist +2 Association →Score statistic
- 17:2617:26, 28 June 2013 diff hist +2 Association →Score statistic
- 17:2617:26, 28 June 2013 diff hist +6 Association No edit summary
- 17:2517:25, 28 June 2013 diff hist 0 Association →Score statistic
- 17:2517:25, 28 June 2013 diff hist −84 Association →Score statistic
- 17:2317:23, 28 June 2013 diff hist −121 Association →Score statistic
- 17:2317:23, 28 June 2013 diff hist +92 Association →Dependency Chain
- 17:2017:20, 28 June 2013 diff hist −81 Association →Score statistic
- 17:1817:18, 28 June 2013 diff hist 0 Association →Dependency Chain
- 17:1817:18, 28 June 2013 diff hist −1 Association →Dependency Chain
- 17:1717:17, 28 June 2013 diff hist −10 Association →Dependency Chain
- 17:1717:17, 28 June 2013 diff hist +499 Association →Example
- 17:1517:15, 28 June 2013 diff hist +2 Association →Dependency Chain
- 17:1417:14, 28 June 2013 diff hist −6 Association →Dependency Chain
- 17:1417:14, 28 June 2013 diff hist +89 Association →Dependency Chain
- 17:1317:13, 28 June 2013 diff hist +43 Association →Dependency Chain
- 17:1217:12, 28 June 2013 diff hist +63 Association →Dependency Chain
- 17:1017:10, 28 June 2013 diff hist +2 Association →Dependency Chain
- 17:1017:10, 28 June 2013 diff hist +60 Association →Dependency Chain
- 17:0917:09, 28 June 2013 diff hist +212 Association →Case control association using allele frequencies
- 17:0417:04, 28 June 2013 diff hist −13 Genotype calling No edit summary
- 17:0117:01, 28 June 2013 diff hist +30 N Template:Cleanup Created page with "This page should be cleaned up" current
- 17:0117:01, 28 June 2013 diff hist +1 Genotype calling No edit summary
- 16:5816:58, 28 June 2013 diff hist +13 Genotype calling No edit summary
- 16:5716:57, 28 June 2013 diff hist −9 Association →Score statistic
- 16:5716:57, 28 June 2013 diff hist +21 Association →Score statistic
- 16:4716:47, 28 June 2013 diff hist +1 Association No edit summary
- 16:4516:45, 28 June 2013 diff hist 0 Association →Case control association using allele frequencies
- 16:4516:45, 28 June 2013 diff hist +8 Association →Case control association using allele frequencies
- 16:4416:44, 28 June 2013 diff hist +4 Association →Case control association using allele frequencies
- 16:4416:44, 28 June 2013 diff hist +2 Association →Case control association using allele frequencies
- 16:4216:42, 28 June 2013 diff hist −65 Association →Case control association using allele frequencies
- 16:4016:40, 28 June 2013 diff hist −74 Association No edit summary
- 16:3116:31, 28 June 2013 diff hist +1 Association →Case control association using allele frequencies
- 16:3016:30, 28 June 2013 diff hist +1 Association →Case control association using allele frequencies
- 16:3016:30, 28 June 2013 diff hist +16 Association →Case control association using allele frequencies
- 16:2816:28, 28 June 2013 diff hist −1 Association →Case control association using allele frequencies
- 16:2816:28, 28 June 2013 diff hist +59 Association →Case control association using allele frequencies
- 16:2516:25, 28 June 2013 diff hist −34 Association No edit summary
- 16:2316:23, 28 June 2013 diff hist −16 Association No edit summary
- 16:2016:20, 28 June 2013 diff hist +146 Association No edit summary
- 16:1216:12, 28 June 2013 diff hist +211 Association No edit summary
- 16:0916:09, 28 June 2013 diff hist 0 Association →example
- 16:0916:09, 28 June 2013 diff hist −2 Association →example
- 16:0816:08, 28 June 2013 diff hist 0 Association No edit summary
- 16:0616:06, 28 June 2013 diff hist −328 Association No edit summary
- 16:0516:05, 28 June 2013 diff hist −30 Association No edit summary
- 16:0416:04, 28 June 2013 diff hist +1 Association No edit summary
- 16:0416:04, 28 June 2013 diff hist −6 Association No edit summary
- 16:0416:04, 28 June 2013 diff hist −48 Association No edit summary
- 16:0316:03, 28 June 2013 diff hist +53 Association No edit summary
- 16:0216:02, 28 June 2013 diff hist 0 Association No edit summary
- 16:0016:00, 28 June 2013 diff hist 0 Association No edit summary
- 15:5915:59, 28 June 2013 diff hist 0 Association No edit summary
- 15:5815:58, 28 June 2013 diff hist +200 Association No edit summary
- 15:5615:56, 28 June 2013 diff hist +46 Association No edit summary
- 15:5415:54, 28 June 2013 diff hist +132 Association No edit summary
- 15:5315:53, 28 June 2013 diff hist +133 Association No edit summary
- 15:5015:50, 28 June 2013 diff hist +4 Association No edit summary
- 15:4915:49, 28 June 2013 diff hist +145 Association No edit summary
- 15:4815:48, 28 June 2013 diff hist +37 Association No edit summary
- 15:4615:46, 28 June 2013 diff hist +76 Association No edit summary
- 15:4515:45, 28 June 2013 diff hist +13 Association No edit summary
- 15:4315:43, 28 June 2013 diff hist −21 Association →output
- 15:2715:27, 28 June 2013 diff hist +4 Association →Score statistic
- 15:2415:24, 28 June 2013 diff hist +341 Skotte2012 No edit summary
- 15:2315:23, 28 June 2013 diff hist +31 Skotte2012 No edit summary
- 15:2115:21, 28 June 2013 diff hist −77 Association →Score statistic
- 15:2115:21, 28 June 2013 diff hist +191 Association →Score statistic
- 15:2015:20, 28 June 2013 diff hist +285 Association →Score statistic
- 15:2015:20, 28 June 2013 diff hist +274 Association →Score statistic
- 15:1715:17, 28 June 2013 diff hist −102 Association →Score statistic
- 15:1715:17, 28 June 2013 diff hist −2 Association No edit summary
- 15:1715:17, 28 June 2013 diff hist +32 Association No edit summary
- 15:1515:15, 28 June 2013 diff hist +145 Association →Score statistic
- 14:5414:54, 28 June 2013 diff hist +52 Kim2011 No edit summary current
- 14:5314:53, 28 June 2013 diff hist +505 Kim2011 No edit summary
- 14:5114:51, 28 June 2013 diff hist −5 Association →Case control association using allele frequencies
- 14:5014:50, 28 June 2013 diff hist +140 Association →Case control association using allele frequencies
- 14:3214:32, 28 June 2013 diff hist 0 Association No edit summary
- 14:2814:28, 28 June 2013 diff hist +60 Association No edit summary
- 14:2614:26, 28 June 2013 diff hist +1 Association No edit summary
- 14:1314:13, 28 June 2013 diff hist −15 Association No edit summary
- 14:1314:13, 28 June 2013 diff hist −15 Association No edit summary
- 13:5813:58, 28 June 2013 diff hist +37 ANGSD No edit summary
- 13:5013:50, 28 June 2013 diff hist +6 Authors No edit summary current
- 13:5013:50, 28 June 2013 diff hist +253 Authors No edit summary
27 June 2013
- 15:2115:21, 27 June 2013 diff hist +85 Filters No edit summary
- 15:2015:20, 27 June 2013 diff hist −108 Filters No edit summary
25 June 2013
- 14:0314:03, 25 June 2013 diff hist +41 Fst PCA No edit summary
- 13:5613:56, 25 June 2013 diff hist −56 Fst PCA No edit summary
- 13:5513:55, 25 June 2013 diff hist −6 Fst PCA No edit summary
- 13:5513:55, 25 June 2013 diff hist +313 Fst PCA No edit summary
- 13:4213:42, 25 June 2013 diff hist +179 N Fst PCA Created page with "Matteo Fumagalli has been working on methods to estimate Fst and doing PCA based on ANGSD output files. =Fst= # Generate .sfs files from each population using ANGSD [[RealSFS..."
- 13:3513:35, 25 June 2013 diff hist +9 MediaWiki:Sidebar No edit summary
- 13:3313:33, 25 June 2013 diff hist +51 HWE and Inbreeding estimates No edit summary
- 13:3213:32, 25 June 2013 diff hist +32 HWE and Inbreeding estimates No edit summary
- 13:2813:28, 25 June 2013 diff hist +1,091 HWE and Inbreeding estimates No edit summary
- 13:2613:26, 25 June 2013 diff hist 0 ANGSD No edit summary
- 13:0413:04, 25 June 2013 diff hist +65 MediaWiki:Sidebar No edit summary
- 09:4809:48, 25 June 2013 diff hist −169 Installation No edit summary
- 09:4709:47, 25 June 2013 diff hist −117 Installation No edit summary
14 June 2013
- 12:1612:16, 14 June 2013 diff hist +236 Change log No edit summary
- 12:0312:03, 14 June 2013 diff hist 0 Installation No edit summary
- 12:0312:03, 14 June 2013 diff hist 0 ANGSD No edit summary
- 01:3201:32, 14 June 2013 diff hist 0 Installation No edit summary
- 01:2601:26, 14 June 2013 diff hist 0 ANGSD No edit summary
- 01:0501:05, 14 June 2013 diff hist +204 Change log →Version notes
25 May 2013
- 02:1602:16, 25 May 2013 diff hist +177 Thetas,Tajima,Neutrality tests No edit summary
24 May 2013
- 16:3916:39, 24 May 2013 diff hist 0 Installation No edit summary
23 May 2013
- 15:2115:21, 23 May 2013 diff hist 0 Installation No edit summary
- 15:2015:20, 23 May 2013 diff hist 0 ANGSD No edit summary
20 May 2013
- 16:5216:52, 20 May 2013 diff hist 0 ANGSD No edit summary
- 16:5216:52, 20 May 2013 diff hist 0 Installation No edit summary
7 May 2013
- 09:3809:38, 7 May 2013 diff hist 0 Installation No edit summary
- 09:3709:37, 7 May 2013 diff hist 0 ANGSD No edit summary
- 00:4200:42, 7 May 2013 diff hist +80 Input →optional arguments
5 May 2013
- 11:4711:47, 5 May 2013 diff hist 0 Installation No edit summary
- 11:4711:47, 5 May 2013 diff hist 0 ANGSD No edit summary
3 May 2013
- 09:5609:56, 3 May 2013 diff hist +1 Tutorial →Understanding angsd output
- 07:4407:44, 3 May 2013 diff hist −3 Tutorial →Getting simple Counts/depth
- 07:3707:37, 3 May 2013 diff hist +35 Tutorial No edit summary
- 03:2803:28, 3 May 2013 diff hist 0 Genotype calling →example
- 03:2403:24, 3 May 2013 diff hist −19 Genotype calling →Genotype calling
- 03:2103:21, 3 May 2013 diff hist 0 Genotype calling →example
- 03:0903:09, 3 May 2013 diff hist −418 Tutorial →Estimating the SFS
- 03:0303:03, 3 May 2013 diff hist +612 Tutorial →Getting simple Counts/depth
- 02:5902:59, 3 May 2013 diff hist −39 Tutorial →Estimating the SFS
- 02:5602:56, 3 May 2013 diff hist +36 Tutorial →Estimating the SFS
- 02:5502:55, 3 May 2013 diff hist −1 Tutorial →Estimating the SFS
- 02:5402:54, 3 May 2013 diff hist +97 Tutorial →Estimating the SFS
- 02:5302:53, 3 May 2013 diff hist 0 Tutorial →Estimating the SFS
- 02:5002:50, 3 May 2013 diff hist −7 Tutorial →Estimating the SFS
- 02:3402:34, 3 May 2013 diff hist +432 Tutorial →Estimating the SFS
- 02:3202:32, 3 May 2013 diff hist −194 Tutorial →Estimating the SFS
- 02:2902:29, 3 May 2013 diff hist +2 Tutorial →Estimating the SFS
- 02:2802:28, 3 May 2013 diff hist −37 Tutorial →Estimating the SFS
- 02:2702:27, 3 May 2013 diff hist +4 Tutorial →Estimating the SFS
- 02:2602:26, 3 May 2013 diff hist +37 Tutorial →Estimating the SFS
- 02:2202:22, 3 May 2013 diff hist +32 Tutorial →Estimating the SFS
- 02:2102:21, 3 May 2013 diff hist −5 Tutorial →Estimating the SFS
- 02:1902:19, 3 May 2013 diff hist 0 N File:TestSFS2.png No edit summary current
- 02:1902:19, 3 May 2013 diff hist +52 N File:TestSFS.png an sfs from bombyx without adjusting for bad quality current
- 02:1702:17, 3 May 2013 diff hist +961 Tutorial →Estimating the SFS
- 02:0102:01, 3 May 2013 diff hist +2,243 Tutorial →Estimating the SFS
- 01:3601:36, 3 May 2013 diff hist +541 Tutorial No edit summary
- 00:4700:47, 3 May 2013 diff hist +56 Quick Start No edit summary
- 00:1500:15, 3 May 2013 diff hist +1,124 Tutorial →Understanding angsd output
- 00:1300:13, 3 May 2013 diff hist +52 Tutorial →Frequencies
- 00:1200:12, 3 May 2013 diff hist +343 Tutorial →Understanding angsd output
- 00:1000:10, 3 May 2013 diff hist +32 Tutorial →Prepare files
- 00:0900:09, 3 May 2013 diff hist −18 Tutorial →Frequencies
- 00:0800:08, 3 May 2013 diff hist +671 Tutorial →Frequencies
- 00:0500:05, 3 May 2013 diff hist +10,738 N Tutorial Created page with "=Prepare files= angsd can work on remote bam files therefore first download a list with 23 unrelated europeans from the 1000genomes project. <pre> wget http://popgen.dk/netstu..."
2 May 2013
- 02:2402:24, 2 May 2013 diff hist −50 Error estimation →options
1 May 2013
- 22:5822:58, 1 May 2013 diff hist 0 Installation →Unix
- 22:5822:58, 1 May 2013 diff hist 0 Installation No edit summary
- 22:5722:57, 1 May 2013 diff hist 0 ANGSD No edit summary
23 April 2013
- 11:2111:21, 23 April 2013 diff hist +45 Bugs →New stuff
21 April 2013
- 03:0503:05, 21 April 2013 diff hist +64 Bugs →Bugs
20 April 2013
- 07:3107:31, 20 April 2013 diff hist −15 Bugs →Bugs
18 April 2013
- 09:2809:28, 18 April 2013 diff hist 0 Installation No edit summary
- 09:2809:28, 18 April 2013 diff hist 0 ANGSD No edit summary
- 04:3404:34, 18 April 2013 diff hist −1 Installation →Unix
- 02:4302:43, 18 April 2013 diff hist 0 Installation No edit summary
- 02:4302:43, 18 April 2013 diff hist 0 ANGSD No edit summary
14 April 2013
- 14:4114:41, 14 April 2013 diff hist +4 Bugs →Bugs
10 April 2013
- 02:5502:55, 10 April 2013 diff hist −2 Installation No edit summary
- 02:5502:55, 10 April 2013 diff hist 0 ANGSD No edit summary
6 April 2013
- 17:5917:59, 6 April 2013 diff hist +3 Installation No edit summary
5 April 2013
- 19:0919:09, 5 April 2013 diff hist −1 Installation →Unix
- 19:0719:07, 5 April 2013 diff hist +119 Installation No edit summary
- 19:0419:04, 5 April 2013 diff hist +13 ANGSD No edit summary
4 April 2013
- 22:2922:29, 4 April 2013 diff hist 0 Installation Undo revision 551 by Thorfinn (talk)
- 22:2822:28, 4 April 2013 diff hist −5 ANGSD No edit summary
- 05:3205:32, 4 April 2013 diff hist 0 Installation No edit summary
- 01:3101:31, 4 April 2013 diff hist −20 ANGSD No edit summary
- 01:3101:31, 4 April 2013 diff hist +1 ANGSD No edit summary
- 01:3101:31, 4 April 2013 diff hist +67 ANGSD No edit summary
- 01:3001:30, 4 April 2013 diff hist +87 ANGSD No edit summary
- 01:2601:26, 4 April 2013 diff hist +184 Change log No edit summary
22 March 2013
- 14:5014:50, 22 March 2013 diff hist +125 Change log No edit summary
- 14:4814:48, 22 March 2013 diff hist −127 m MediaWiki:Sitenotice No edit summary
- 14:4714:47, 22 March 2013 diff hist −2 Installation No edit summary
- 14:4714:47, 22 March 2013 diff hist 0 ANGSD No edit summary
19 March 2013
- 13:3013:30, 19 March 2013 diff hist −135 Allele Counts No edit summary
- 13:3013:30, 19 March 2013 diff hist +17 MediaWiki:Sitenotice No edit summary
- 13:2913:29, 19 March 2013 diff hist +100 MediaWiki:Sitenotice No edit summary
- 13:2813:28, 19 March 2013 diff hist +10 MediaWiki:Sitenotice No edit summary
18 March 2013
- 19:3819:38, 18 March 2013 diff hist +32 Allele Counts No edit summary
- 19:3819:38, 18 March 2013 diff hist +104 Allele Counts No edit summary
- 19:3719:37, 18 March 2013 diff hist +107 Filters No edit summary
15 March 2013
- 21:1121:11, 15 March 2013 diff hist +1 Filters →Warning
- 21:1021:10, 15 March 2013 diff hist +15 Filters →Warning
- 21:0921:09, 15 March 2013 diff hist +599 Filters No edit summary
- 19:5019:50, 15 March 2013 diff hist 0 ANGSD No edit summary
- 19:4919:49, 15 March 2013 diff hist +44 Change log →Version notes
- 19:4919:49, 15 March 2013 diff hist +1 Installation No edit summary
- 19:3219:32, 15 March 2013 diff hist −1 Installation No edit summary
- 17:4717:47, 15 March 2013 diff hist +1 Installation →Unix
- 17:4617:46, 15 March 2013 diff hist +1 Installation No edit summary
- 17:4617:46, 15 March 2013 diff hist +1 ANGSD No edit summary
7 March 2013
- 14:1214:12, 7 March 2013 diff hist +52 Input →optional arguments
- 11:2911:29, 7 March 2013 diff hist +114 Change log No edit summary
- 11:2811:28, 7 March 2013 diff hist +2,321 Change log No edit summary
- 11:2311:23, 7 March 2013 diff hist 0 Installation →Install
- 11:2211:22, 7 March 2013 diff hist −1 Installation No edit summary
- 11:2111:21, 7 March 2013 diff hist 0 ANGSD No edit summary
14 February 2013
- 16:3116:31, 14 February 2013 diff hist +5 Filters No edit summary
- 16:3116:31, 14 February 2013 diff hist +30 Filters No edit summary
8 February 2013
- 13:3913:39, 8 February 2013 diff hist +1 Depth →Depth
1 February 2013
- 14:3314:33, 1 February 2013 diff hist +43 Bugs No edit summary
- 14:3214:32, 1 February 2013 diff hist +69 Bugs No edit summary
31 January 2013
- 13:1813:18, 31 January 2013 diff hist −1 Thetas,Tajima,Neutrality tests No edit summary
22 January 2013
- 01:4801:48, 22 January 2013 diff hist +47 Allele Counts →options
21 January 2013
- 16:3616:36, 21 January 2013 diff hist +76 Major Minor No edit summary
- 16:0116:01, 21 January 2013 diff hist 0 Major Minor →arguments
- 16:0116:01, 21 January 2013 diff hist +204 Major Minor →arguments
- 15:5515:55, 21 January 2013 diff hist −2 Major Minor No edit summary
- 15:5515:55, 21 January 2013 diff hist +69 Major Minor →Inferring Major and Minor alleles
- 15:5115:51, 21 January 2013 diff hist +157 Major Minor No edit summary
- 15:4915:49, 21 January 2013 diff hist +2 Allele Frequencies No edit summary
- 15:4815:48, 21 January 2013 diff hist −1 Allele Frequencies No edit summary
- 15:4815:48, 21 January 2013 diff hist +18 Allele Frequencies No edit summary
- 15:4715:47, 21 January 2013 diff hist +140 Allele Frequencies No edit summary
- 15:4515:45, 21 January 2013 diff hist +2 Allele Frequencies No edit summary
- 15:4515:45, 21 January 2013 diff hist +95 Allele Frequencies No edit summary
- 15:4015:40, 21 January 2013 diff hist +55 Allele Frequencies No edit summary
- 15:3915:39, 21 January 2013 diff hist +38 Allele Frequencies No edit summary
16 January 2013
- 19:3019:30, 16 January 2013 diff hist +70 Genotype calling →options
- 19:2919:29, 16 January 2013 diff hist +1 Installation No edit summary
- 19:2919:29, 16 January 2013 diff hist −4 ANGSD No edit summary
4 January 2013
- 14:5014:50, 4 January 2013 diff hist −14 Filters →Major minor
3 January 2013
- 02:5002:50, 3 January 2013 diff hist +61 N Thorfinn Created page with "Check keepsites in -filter check leak in get3likes Thorfinn"
28 December 2012
- 20:0820:08, 28 December 2012 diff hist +133 Bugs No edit summary
- 20:0520:05, 28 December 2012 diff hist +39 Bugs No edit summary
19 December 2012
- 21:3021:30, 19 December 2012 diff hist +155 Filters →Selected Sites
- 21:2821:28, 19 December 2012 diff hist −5 Filters →Selected Sites
- 21:2821:28, 19 December 2012 diff hist +310 Filters →Selected Sites
- 21:1021:10, 19 December 2012 diff hist +21 SFS Estimation No edit summary
- 21:0421:04, 19 December 2012 diff hist +214 SFS Estimation No edit summary
18 December 2012
- 15:2615:26, 18 December 2012 diff hist +18 MediaWiki:Sidebar No edit summary
- 15:2315:23, 18 December 2012 diff hist 0 MediaWiki:Sidebar No edit summary
- 15:2315:23, 18 December 2012 diff hist +5 MediaWiki:Sidebar No edit summary
- 15:2215:22, 18 December 2012 diff hist 0 MediaWiki:Sidebar No edit summary
- 15:1815:18, 18 December 2012 diff hist +7 MediaWiki:Sidebar No edit summary
- 15:1715:17, 18 December 2012 diff hist +8 MediaWiki:Sidebar No edit summary
- 03:3203:32, 18 December 2012 diff hist +445 N Memory Usage Created page with "For large sample sizes and if many threads are allocated to the program the memory usage can become severe. The filewriting has to be done in the correct order, and if some g..." current
- 03:1003:10, 18 December 2012 diff hist +131 Thetas,Tajima,Neutrality tests →.thetas.gz.pestPG
- 03:0903:09, 18 December 2012 diff hist −1 Thetas,Tajima,Neutrality tests →.thetas.gz.pestPG
- 03:0803:08, 18 December 2012 diff hist +2,618 Thetas,Tajima,Neutrality tests →Example Output
- 03:0703:07, 18 December 2012 diff hist +108 Thetas,Tajima,Neutrality tests →Example Output
- 03:0003:00, 18 December 2012 diff hist +6 Thetas,Tajima,Neutrality tests No edit summary
- 03:0003:00, 18 December 2012 diff hist +69 Thetas,Tajima,Neutrality tests →Example Output
- 02:5502:55, 18 December 2012 diff hist −2 Thetas,Tajima,Neutrality tests →Example Output
- 02:5502:55, 18 December 2012 diff hist +1,668 Thetas,Tajima,Neutrality tests No edit summary
- 02:5302:53, 18 December 2012 diff hist +2 Thetas,Tajima,Neutrality tests No edit summary
- 02:5302:53, 18 December 2012 diff hist +508 Thetas,Tajima,Neutrality tests No edit summary
- 02:4402:44, 18 December 2012 diff hist +245 Thetas,Tajima,Neutrality tests No edit summary
- 02:4002:40, 18 December 2012 diff hist +59 N Thetas,Tajima,Neutrality tests Created page with "Angsd can estimate the Tajimas D and other neutrality test."
16 December 2012
- 21:3221:32, 16 December 2012 diff hist −2 Installation No edit summary
- 21:3021:30, 16 December 2012 diff hist 0 ANGSD No edit summary
11 December 2012
- 22:1022:10, 11 December 2012 diff hist +130 Bugs No edit summary
- 22:0622:06, 11 December 2012 diff hist +24 Bugs No edit summary
- 18:1318:13, 11 December 2012 diff hist +23 Filters →Number of non missing individuals
5 December 2012
- 23:3023:30, 5 December 2012 diff hist +4 Bugs →Limitation
- 23:3023:30, 5 December 2012 diff hist +130 Bugs →Limitation
- 23:0823:08, 5 December 2012 diff hist +34 Bugs No edit summary
- 19:2219:22, 5 December 2012 diff hist +90 Allele Frequencies →.mafs
- 19:2019:20, 5 December 2012 diff hist +46 Bugs No edit summary
- 18:5918:59, 5 December 2012 diff hist +2 Allele Frequencies →.mafs
- 18:5918:59, 5 December 2012 diff hist +462 Allele Frequencies →.mafs
4 December 2012
- 18:0218:02, 4 December 2012 diff hist +103 Bugs No edit summary
3 December 2012
- 14:2014:20, 3 December 2012 diff hist −76 Genotype Likelihoods →output genotype likelihoods
- 11:5611:56, 3 December 2012 diff hist +130 Genotype Likelihoods →output genotype likelihoods
30 November 2012
- 19:4619:46, 30 November 2012 diff hist +143 Bugs No edit summary
- 19:4119:41, 30 November 2012 diff hist +49 Bugs No edit summary
28 November 2012
- 12:4012:40, 28 November 2012 diff hist −43 Installation No edit summary
- 12:3012:30, 28 November 2012 diff hist +36 Bugs No edit summary
18 November 2012
- 00:1500:15, 18 November 2012 diff hist +24 Bugs No edit summary
16 November 2012
- 17:1917:19, 16 November 2012 diff hist +87 Bugs No edit summary
15 November 2012
- 00:4300:43, 15 November 2012 diff hist +145 SFS Estimation →Example
1 November 2012
- 15:4915:49, 1 November 2012 diff hist +128 Bugs No edit summary
- 14:4214:42, 1 November 2012 diff hist +59 Bugs No edit summary
- 14:3914:39, 1 November 2012 diff hist +96 Bugs No edit summary
24 October 2012
- 13:0013:00, 24 October 2012 diff hist +191 Glf files No edit summary current
23 October 2012
- 23:3923:39, 23 October 2012 diff hist +89 ANGSD No edit summary
- 22:0222:02, 23 October 2012 diff hist −135 Bugs No edit summary
- 21:5721:57, 23 October 2012 diff hist +297 Bugs No edit summary
- 21:2621:26, 23 October 2012 diff hist +34 Installation →Download
- 21:1421:14, 23 October 2012 diff hist +2 Quick Start →Examples
- 21:1321:13, 23 October 2012 diff hist +661 N Quick Start Created page with "==Whats on this page== This page will contain som random examples which can be used as a quickstart. ===Examples=== Assuming you have a list of bamfiles in in file: 'list.tx..."
- 21:0321:03, 23 October 2012 diff hist −54 Authors No edit summary
- 21:0021:00, 23 October 2012 diff hist −5 Authors No edit summary
- 21:0021:00, 23 October 2012 diff hist +85 Authors No edit summary
- 20:5820:58, 23 October 2012 diff hist −2 Authors →Disclaimer
- 20:5720:57, 23 October 2012 diff hist +97 Authors →Disclaimer
- 20:5620:56, 23 October 2012 diff hist +33 Authors →Disclaimer
- 20:5320:53, 23 October 2012 diff hist +93 Authors →Disclaimer
- 20:5120:51, 23 October 2012 diff hist +78 Authors No edit summary
- 20:4020:40, 23 October 2012 diff hist +2 Authors No edit summary
- 20:4020:40, 23 October 2012 diff hist +34 Authors No edit summary
- 19:1319:13, 23 October 2012 diff hist +86 Introduction No edit summary current
- 19:1019:10, 23 October 2012 diff hist +1 Authors No edit summary
- 19:0519:05, 23 October 2012 diff hist +80 N Authors Created page with "Thorfinn Korneliussen thorfinn@binf.ku.dk anders gaylordsen albrecht@binf.ku.dk"
- 18:3718:37, 23 October 2012 diff hist +88 Bugs No edit summary
- 09:1509:15, 23 October 2012 diff hist 0 Introduction No edit summary
- 09:1509:15, 23 October 2012 diff hist +1 Introduction No edit summary
- 09:1409:14, 23 October 2012 diff hist +292 Introduction No edit summary
- 09:0809:08, 23 October 2012 diff hist +39 Introduction No edit summary
- 09:0709:07, 23 October 2012 diff hist +2 Introduction No edit summary
- 09:0709:07, 23 October 2012 diff hist +128 Introduction No edit summary
- 09:0509:05, 23 October 2012 diff hist +195 N Introduction Created page with "Assuming you have a list of bamfiles in in file: 'list.txt' and you want the genotype likelihoods for position 12500000 on chromosome 8. <pre> ./angsd -bam list.txt -GL 1 -r ..."
20 October 2012
- 23:4723:47, 20 October 2012 diff hist +101 Installation →Download
- 05:2105:21, 20 October 2012 diff hist +9 Installation →Download
- 05:2005:20, 20 October 2012 diff hist 0 Installation →Download
- 05:1705:17, 20 October 2012 diff hist +185 Installation →Download
- 04:1804:18, 20 October 2012 diff hist +118 Bugs No edit summary
18 October 2012
- 04:0404:04, 18 October 2012 diff hist +44 Bugs No edit summary
- 04:0004:00, 18 October 2012 diff hist +38 Bugs No edit summary
- 03:0403:04, 18 October 2012 diff hist +302 Bugs No edit summary
17 October 2012
- 23:4123:41, 17 October 2012 diff hist +62 SFS Estimation →Example
- 23:3923:39, 17 October 2012 diff hist −13 Error estimation →Error estimation from polymorphic sites
- 23:3823:38, 17 October 2012 diff hist +107 Change log →Version notes
- 23:3523:35, 17 October 2012 diff hist +1 Installation →Unix
- 23:3523:35, 17 October 2012 diff hist +1 Installation →Download
- 23:3423:34, 17 October 2012 diff hist +1 ANGSD No edit summary
- 22:0422:04, 17 October 2012 diff hist −161 ANGSD →About
- 22:0122:01, 17 October 2012 diff hist −1 ANGSD →About
- 22:0122:01, 17 October 2012 diff hist +389 ANGSD →About
16 October 2012
- 17:5017:50, 16 October 2012 diff hist +1 Bugs No edit summary
- 17:5017:50, 16 October 2012 diff hist +83 Bugs No edit summary
15 October 2012
- 12:1212:12, 15 October 2012 diff hist +9 Input →optional arguments
14 October 2012
- 02:0402:04, 14 October 2012 diff hist +54 N Bugs Created page with "1. check numSites==0 in all generals: derived classes."
12 October 2012
- 00:2300:23, 12 October 2012 diff hist +1,031 Depth →Output
- 00:2100:21, 12 October 2012 diff hist +4 Depth →Example
- 00:2100:21, 12 October 2012 diff hist +202 Depth →Example
- 00:1800:18, 12 October 2012 diff hist 0 Depth →Output
- 00:1800:18, 12 October 2012 diff hist +152 Depth →Output
- 00:1600:16, 12 October 2012 diff hist +483 Depth →Output
- 00:1500:15, 12 October 2012 diff hist −1,204 Depth →Output
- 00:1300:13, 12 October 2012 diff hist +1,632 Depth →Output
- 00:1200:12, 12 October 2012 diff hist +320 Depth No edit summary
11 October 2012
- 23:2423:24, 11 October 2012 diff hist +13 Error estimation →Error estimation from polymorphic sites
- 23:2123:21, 11 October 2012 diff hist +167 Error estimation →Output
- 23:1523:15, 11 October 2012 diff hist +95 Error estimation →options
- 23:1423:14, 11 October 2012 diff hist +164 Error estimation →Output
- 23:0923:09, 11 October 2012 diff hist +1,032 Error estimation →options
- 22:3522:35, 11 October 2012 diff hist +240 Error estimation →Error estimation from polymorphic sites
- 22:3222:32, 11 October 2012 diff hist +272 Error estimation →Error estimation from polymorphic sites
- 22:2822:28, 11 October 2012 diff hist 0 Citing angsd →Maf estimation from counts of alleles
- 22:2722:27, 11 October 2012 diff hist +62 Citing angsd →Methods
- 15:0415:04, 11 October 2012 diff hist +52 Major Minor →From genotype likelihood data
- 15:0415:04, 11 October 2012 diff hist −5 Major Minor →From genotype likelihood data
10 October 2012
- 18:3718:37, 10 October 2012 diff hist +43 SFS Estimation No edit summary
- 18:3418:34, 10 October 2012 diff hist +11 SFS Estimation No edit summary
- 18:3218:32, 10 October 2012 diff hist +39 SFS Estimation No edit summary
- 18:3118:31, 10 October 2012 diff hist +4 SFS Estimation →Example
- 18:3018:30, 10 October 2012 diff hist +202 SFS Estimation No edit summary
- 18:2418:24, 10 October 2012 diff hist 0 Citing angsd No edit summary
- 18:2318:23, 10 October 2012 diff hist +4 SFS Estimation →Example
- 18:2318:23, 10 October 2012 diff hist +252 SFS Estimation →Example
- 18:2118:21, 10 October 2012 diff hist +148 SFS Estimation No edit summary
- 18:1718:17, 10 October 2012 diff hist +570 SFS Estimation No edit summary
- 15:2615:26, 10 October 2012 diff hist +4 SFS Estimation No edit summary
- 15:2315:23, 10 October 2012 diff hist +24 SFS Estimation →realSFS
- 15:1815:18, 10 October 2012 diff hist +95 SFS Estimation →realSFS
- 15:0815:08, 10 October 2012 diff hist +14 SFS Estimation →realSFS
- 15:0715:07, 10 October 2012 diff hist −1,036 SFS Estimation No edit summary
- 14:2314:23, 10 October 2012 diff hist +98 SFS Estimation No edit summary
- 14:2214:22, 10 October 2012 diff hist −6 Beagle input No edit summary
- 14:2214:22, 10 October 2012 diff hist +23 Beagle input No edit summary
- 14:1414:14, 10 October 2012 diff hist +77 Citing angsd →Methods
- 14:1314:13, 10 October 2012 diff hist +84 Nielsen2012 No edit summary
- 14:1214:12, 10 October 2012 diff hist +85 Nielsen2012 No edit summary
- 14:1114:11, 10 October 2012 diff hist +105 N Nielsen2012 Created page with "SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data"
- 14:0614:06, 10 October 2012 diff hist 0 Genotype Likelihoods →Genotype likelihoods from alignments
- 14:0614:06, 10 October 2012 diff hist −1 Genotype Likelihoods →Genotype likelihoods from alignments
- 14:0314:03, 10 October 2012 diff hist +1 Installation →Unix
- 14:0214:02, 10 October 2012 diff hist 0 Installation →Download
- 14:0214:02, 10 October 2012 diff hist −2 ANGSD No edit summary
25 September 2012
- 18:4118:41, 25 September 2012 diff hist +450 Filters →Selected Sites
- 17:3217:32, 25 September 2012 diff hist +1 Installation →Download
- 17:3217:32, 25 September 2012 diff hist 0 ANGSD No edit summary
- 04:0004:00, 25 September 2012 diff hist +76 Genotype Likelihoods →output genotype likelihoods
- 03:3803:38, 25 September 2012 diff hist +211 Change log →Version notes
- 03:3703:37, 25 September 2012 diff hist +56 Genotype Likelihoods →soapSNP
- 03:3503:35, 25 September 2012 diff hist +81 Genotype Likelihoods →options
- 03:3503:35, 25 September 2012 diff hist −166 Genotype Likelihoods →options
- 03:3403:34, 25 September 2012 diff hist +1 ANGSD No edit summary
23 September 2012
- 00:3500:35, 23 September 2012 diff hist −60 SFS Estimation →realSFS
22 September 2012
- 20:4320:43, 22 September 2012 diff hist +1 Installation →Unix
- 20:4220:42, 22 September 2012 diff hist +2 Installation →Download
- 20:4220:42, 22 September 2012 diff hist +86 Installation →Download
- 20:3920:39, 22 September 2012 diff hist +45 ANGSD No edit summary
2 July 2012
- 11:3711:37, 2 July 2012 diff hist +559 Genotype Likelihoods →soapSNP
29 June 2012
- 15:3715:37, 29 June 2012 diff hist −16 Regionfile No edit summary current
- 15:3615:36, 29 June 2012 diff hist −1 Regionfile No edit summary
- 15:3615:36, 29 June 2012 diff hist +664 N Regionfile Created page with "When your inputfile is bam files, then you can specify region You can specify a specific region using the following 3 ways: <examople> ./angsd -bam bamfiles.list -r chr20: ...."
22 June 2012
- 22:1822:18, 22 June 2012 diff hist +137 N Glf files Created page with "DRAGON ;-doGlf 1; tglf binary 10xdouble per sample ;-doGlf 2; beagle output gz requires -doMajorMinor 1/2 ;-doGlf otehrwise text output"
- 16:0316:03, 22 June 2012 diff hist +3 Genotype Likelihoods →Kim et al.
- 16:0216:02, 22 June 2012 diff hist +22 Genotype Likelihoods →soapSNP
19 June 2012
- 14:0414:04, 19 June 2012 diff hist +587 Filters No edit summary
- 14:0114:01, 19 June 2012 diff hist +900 Filters No edit summary
- 13:5813:58, 19 June 2012 diff hist +428 Filters No edit summary
- 12:4812:48, 19 June 2012 diff hist +114 Filters No edit summary
- 12:4212:42, 19 June 2012 diff hist 0 Filters No edit summary
- 12:4212:42, 19 June 2012 diff hist −9 Filters No edit summary
- 12:4212:42, 19 June 2012 diff hist +2 Filters No edit summary
- 12:4112:41, 19 June 2012 diff hist +342 N Filters Created page with "In most analysis you are only interested in a subset of sites and not all sites. Currently we have the following filter options. 1. ;-minMaf float: only work with sites with..."
- 12:3412:34, 19 June 2012 diff hist +107 SNP Calling No edit summary current
- 12:3312:33, 19 June 2012 diff hist +444 SNP Calling No edit summary
- 12:2012:20, 19 June 2012 diff hist +94 Allele Frequencies →Estimator from sequencing data
- 12:1812:18, 19 June 2012 diff hist +73 Genotype calling No edit summary
- 12:1512:15, 19 June 2012 diff hist +107 N SNP Calling Created page with "angsd can estimate and LRT for the site being variable. This works in tandem with -doMAF and -doMajorMinor."
- 12:0112:01, 19 June 2012 diff hist −265 SFS Estimation →Full example for simulating nextgen data and estimating SFS (somewhat deprecated should use sfstools now)
- 11:3411:34, 19 June 2012 diff hist +31 SFS Estimation →realSFS
- 11:3311:33, 19 June 2012 diff hist −41 SFS Estimation →realSFS
- 11:3111:31, 19 June 2012 diff hist −2 Input →tglf
- 11:3011:30, 19 June 2012 diff hist −6 Input →tglf
- 11:3011:30, 19 June 2012 diff hist +258 Input →tglf
- 11:2711:27, 19 June 2012 diff hist +10 Input →genotype likelihood files
- 11:2611:26, 19 June 2012 diff hist +461 Input →genotype likelihood files
- 11:2011:20, 19 June 2012 diff hist 0 Input →optional arguments
- 11:1911:19, 19 June 2012 diff hist −38 Input →bam files
- 11:1711:17, 19 June 2012 diff hist +1 Input No edit summary
14 June 2012
- 13:3713:37, 14 June 2012 diff hist +7 N Major Minor Created page with "SuX CuX"
1 June 2012
- 09:1509:15, 1 June 2012 diff hist +126 ANGSD →Commands
- 09:1309:13, 1 June 2012 diff hist +22 ANGSD →Commands
- 09:1209:12, 1 June 2012 diff hist +293 ANGSD →Commands
- 09:0809:08, 1 June 2012 diff hist +20 ANGSD No edit summary