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