ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
User contributions for Thorfinn
Jump to navigation
Jump to search
4 December 2015
- 15:0715:07, 4 December 2015 diff hist −130 ANGSD →Synopsis current
- 14:5814:58, 4 December 2015 diff hist +1 Quick Start No edit summary current
- 14:5814:58, 4 December 2015 diff hist −1 Quick Start No edit summary
- 14:5614:56, 4 December 2015 diff hist +72 Major Minor →Brief Overview current
- 14:5314:53, 4 December 2015 diff hist +1,140 RealSFS →Brief overview
- 14:5214:52, 4 December 2015 diff hist −129 RealSFS No edit summary
- 14:5114:51, 4 December 2015 diff hist 0 Input →options
- 14:4514:45, 4 December 2015 diff hist +73 Input →Pileup files
- 10:4210:42, 4 December 2015 diff hist +16 Input →Genotype Likelihood Files
- 10:4010:40, 4 December 2015 diff hist +1 Input →Genotype Likelihood Files
- 10:3610:36, 4 December 2015 diff hist +35 Input →glf
- 10:3610:36, 4 December 2015 diff hist +54 Input →glf
- 10:2810:28, 4 December 2015 diff hist +30 Input →glf
- 10:1010:10, 4 December 2015 diff hist +428 Input →Brief Overview
- 10:0510:05, 4 December 2015 diff hist −1 ANGSD No edit summary
- 10:0510:05, 4 December 2015 diff hist −2 ANGSD No edit summary
- 10:0510:05, 4 December 2015 diff hist −217 ANGSD No edit summary
- 10:0410:04, 4 December 2015 diff hist −4 ANGSD No edit summary
- 10:0110:01, 4 December 2015 diff hist 0 Input No edit summary
26 November 2015
- 14:2214:22, 26 November 2015 diff hist +252 Error estimation →Output
23 November 2015
- 13:2613:26, 23 November 2015 diff hist +495 Fst →Sliding Window output
20 November 2015
- 14:2914:29, 20 November 2015 diff hist −11 SFS Estimation No edit summary
- 14:2914:29, 20 November 2015 diff hist +354 SFS Estimation →How to plot
- 04:1804:18, 20 November 2015 diff hist 0 Installation No edit summary
- 04:1604:16, 20 November 2015 diff hist +60 Change log →Latests
- 04:1604:16, 20 November 2015 diff hist 0 MediaWiki:Sitenotice No edit summary
- 03:5003:50, 20 November 2015 diff hist +53 SFS Estimation No edit summary
16 November 2015
- 16:0016:00, 16 November 2015 diff hist +1 Sites →Bedfiles? current
- 15:0415:04, 16 November 2015 diff hist +99 Abbababa No edit summary
14 November 2015
- 03:2803:28, 14 November 2015 diff hist +84 Installation No edit summary
- 03:1303:13, 14 November 2015 diff hist 0 Installation →Install from github
- 03:1203:12, 14 November 2015 diff hist 0 Installation →Unix
- 02:5302:53, 14 November 2015 diff hist +41 Installation →Install from github
- 02:4902:49, 14 November 2015 diff hist +38 Installation →Unix
7 November 2015
- 01:5501:55, 7 November 2015 diff hist −249 ANGSD No edit summary
- 01:5501:55, 7 November 2015 diff hist +249 ANGSD No edit summary
19 October 2015
- 18:5218:52, 19 October 2015 diff hist −79 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 18:5218:52, 19 October 2015 diff hist +1 Thetas,Tajima,Neutrality tests →Step 1: Finding a 'global estimate' of the SFS
- 18:5118:51, 19 October 2015 diff hist +1 Thetas,Tajima,Neutrality tests updatated the examples for latest version of realSFS, thanks kebi
- 18:5018:50, 19 October 2015 diff hist +1 Thetas,Tajima,Neutrality tests →Full command list for below examples
13 October 2015
- 01:0601:06, 13 October 2015 diff hist +162 Fst No edit summary
8 October 2015
- 18:3818:38, 8 October 2015 diff hist −4 Pbs No edit summary current
31 August 2015
- 10:0810:08, 31 August 2015 diff hist +149 Citing angsd →Contamination current
24 August 2015
- 14:1714:17, 24 August 2015 diff hist 0 Input →Brief Overview
21 August 2015
30 July 2015
- 19:2219:22, 30 July 2015 diff hist +65 Fst No edit summary
- 19:2219:22, 30 July 2015 diff hist +9 Fst No edit summary
- 19:2119:21, 30 July 2015 diff hist +244 Fst No edit summary
- 16:4016:40, 30 July 2015 diff hist 0 Installation →Unix
- 16:4016:40, 30 July 2015 diff hist 0 Installation →Download and Installation
- 16:3816:38, 30 July 2015 diff hist −102 MediaWiki:Sitenotice No edit summary
- 16:2716:27, 30 July 2015 diff hist +6,807 N Fst correctness Created page with "= 3 Populations simulated data= <pre> msms -ms 44 10 -t 930 -r 400 -I 3 12 14 18 -n 1 1.682020 -n 2 3.736830 -n 3 7.292050 -eg 0 2 116.010723 -eg 0 3 160.246047 -ma x 0.881098..." current
- 16:2616:26, 30 July 2015 diff hist −6,809 Fst No edit summary
- 16:2216:22, 30 July 2015 diff hist +242 N PCA Created page with "Matteo Fumagalli has been working on methods for doing PCA/Covariance based on ANGSD output files. The main documentation for this is found here: https://github.com/mfumagall..."
- 16:2116:21, 30 July 2015 diff hist −24 Fst PCA No edit summary current
- 16:2116:21, 30 July 2015 diff hist +86 Fst PCA No edit summary
- 16:2016:20, 30 July 2015 diff hist −10,708 Fst PCA No edit summary
- 16:1916:19, 30 July 2015 diff hist +3 MediaWiki:Sidebar No edit summary
- 16:1716:17, 30 July 2015 diff hist −2 Fst →3 Populations simulated data
- 16:1616:16, 30 July 2015 diff hist −2 Fst →Sliding Window output
- 16:1616:16, 30 July 2015 diff hist −2 Fst →3 Populations real data
- 16:1616:16, 30 July 2015 diff hist −421 Fst No edit summary
- 16:1416:14, 30 July 2015 diff hist −336 Fst No edit summary
- 16:1416:14, 30 July 2015 diff hist +11,331 N Fst Created page with "Matteo Fumagalli has been working on methods to estimate Fst and doing PCA/Covariance based on ANGSD output files. The main documentation for this is found here: https://gith..."
- 15:5615:56, 30 July 2015 diff hist +247 Fst PCA No edit summary
- 15:5415:54, 30 July 2015 diff hist +111 N Pbs Created page with "See Fst PCA for examples on how to obtain the pbs statistics in the fst output if you supply 3 populations."
- 15:5315:53, 30 July 2015 diff hist +44 MediaWiki:Sidebar No edit summary
- 15:5115:51, 30 July 2015 diff hist +414 Fst PCA →Sliding Window output
- 15:5015:50, 30 July 2015 diff hist −220 Fst PCA →3 Populations real data
- 15:5015:50, 30 July 2015 diff hist +374 Fst PCA →3 Populations real data
- 15:4815:48, 30 July 2015 diff hist +98 Fst PCA →3 Populations real data
- 14:4514:45, 30 July 2015 diff hist −2 Fst PCA →3 Populations real data
- 14:4214:42, 30 July 2015 diff hist −3 Fst PCA →3 Populations real data
- 14:4114:41, 30 July 2015 diff hist −3 Fst PCA →3 Populations real data
29 July 2015
- 16:3416:34, 29 July 2015 diff hist +49 SFS Estimation →Options
28 July 2015
- 15:4715:47, 28 July 2015 diff hist −4 Genotype Likelihoods →SYK genotype likelihoods
- 15:4615:46, 28 July 2015 diff hist +1,652 Genotype Likelihoods No edit summary
22 July 2015
- 18:5718:57, 22 July 2015 diff hist +3 RealSFS No edit summary
- 18:5718:57, 22 July 2015 diff hist −2 RealSFS No edit summary
- 18:5618:56, 22 July 2015 diff hist +68 RealSFS No edit summary
- 18:5218:52, 22 July 2015 diff hist +11 RealSFS →2dsfs
- 18:5218:52, 22 July 2015 diff hist +11 RealSFS →1d SFS
- 18:5218:52, 22 July 2015 diff hist +295 RealSFS →Printing the SAF
- 18:5018:50, 22 July 2015 diff hist +178 RealSFS →Brief overview
- 18:4618:46, 22 July 2015 diff hist +157 RealSFS No edit summary
- 18:4318:43, 22 July 2015 diff hist +2 SFS Estimation →Using NGStools
- 18:4318:43, 22 July 2015 diff hist +110 SFS Estimation →safv3 comparison
- 18:4218:42, 22 July 2015 diff hist +222 RealSFS →Using NGStools/NGSpopgen
- 18:3918:39, 22 July 2015 diff hist +288 RealSFS →Using NGStools
- 18:3518:35, 22 July 2015 diff hist +18 RealSFS →-nSites
9 July 2015
- 15:4815:48, 9 July 2015 diff hist +59 SFS Estimation →Brief Overview
- 15:4715:47, 9 July 2015 diff hist +235 RealSFS →NB
20 June 2015
- 10:2610:26, 20 June 2015 diff hist +26 MediaWiki:Sidebar No edit summary
- 10:2310:23, 20 June 2015 diff hist +84 N NgsRelate Created page with "ngsrelate has its very own website http://www.popgen.dk/software/index.php/NgsRelate" current
18 June 2015
- 15:0915:09, 18 June 2015 diff hist +14 MediaWiki:Sitenotice No edit summary
- 15:0615:06, 18 June 2015 diff hist +403 Installation Undo revision 2514 by Thorfinn (talk)
- 14:4914:49, 18 June 2015 diff hist +1 MediaWiki:Sitenotice No edit summary
- 14:4914:49, 18 June 2015 diff hist +87 MediaWiki:Sitenotice No edit summary
- 12:2812:28, 18 June 2015 diff hist −403 Installation No edit summary
17 June 2015
- 17:4217:42, 17 June 2015 diff hist +2 Fst PCA →Sliding Window output
- 17:4217:42, 17 June 2015 diff hist +69 Fst PCA →3 Populations real data
- 17:4117:41, 17 June 2015 diff hist +208 Fst PCA →3 Populations real data
- 17:3917:39, 17 June 2015 diff hist +871 Fst PCA →3 Populations real data
- 17:3317:33, 17 June 2015 diff hist +1 Fst PCA →Two Populations real data
- 17:3017:30, 17 June 2015 diff hist +1 Fst PCA →3 Populations real data
- 17:3017:30, 17 June 2015 diff hist +106 Fst PCA →3 Populations real data
- 17:2517:25, 17 June 2015 diff hist +158 Fst PCA →3 Populations real data
- 17:2217:22, 17 June 2015 diff hist +1 Fst PCA →Two Populations real data
- 17:2217:22, 17 June 2015 diff hist +757 Fst PCA →New Fancy Version
- 17:2017:20, 17 June 2015 diff hist +274 Fst PCA →Two Populations real data
- 17:1417:14, 17 June 2015 diff hist 0 Fst PCA →new fancy version
- 17:1417:14, 17 June 2015 diff hist +37 Fst PCA →New Fancy Method (sim data)
- 17:1317:13, 17 June 2015 diff hist −307 Fst PCA No edit summary
- 17:1117:11, 17 June 2015 diff hist +20 Fst PCA →2pops
- 17:1117:11, 17 June 2015 diff hist +2 Fst PCA →2pops
- 17:1117:11, 17 June 2015 diff hist −1 Fst PCA →new fancy version
- 17:1017:10, 17 June 2015 diff hist +47 Fst PCA No edit summary
- 17:0817:08, 17 June 2015 diff hist +11 Fst PCA No edit summary
16 June 2015
- 21:5621:56, 16 June 2015 diff hist +1,514 Fst PCA →3pops
- 21:4021:40, 16 June 2015 diff hist 0 Fst PCA →3pops
- 21:0421:04, 16 June 2015 diff hist +776 Fst PCA →3pops
- 20:5620:56, 16 June 2015 diff hist +465 Fst PCA →3pops
- 20:5320:53, 16 June 2015 diff hist +144 Fst PCA →3pops
- 20:4620:46, 16 June 2015 diff hist +100 Fst PCA →3pops
- 19:2019:20, 16 June 2015 diff hist +7 Fst PCA →new fancy version
- 17:4517:45, 16 June 2015 diff hist +339 Fst PCA →new fancy version
- 14:3814:38, 16 June 2015 diff hist +331 Fst PCA →new fancy version
12 June 2015
- 21:5421:54, 12 June 2015 diff hist 0 MediaWiki:Sitenotice No edit summary
- 15:2115:21, 12 June 2015 diff hist +60 Change log →Latests
- 15:2015:20, 12 June 2015 diff hist 0 Installation No edit summary
- 13:5213:52, 12 June 2015 diff hist +78 Fst PCA No edit summary
10 June 2015
7 June 2015
- 23:1023:10, 7 June 2015 diff hist +224 Fst PCA →new fancy version
- 23:0523:05, 7 June 2015 diff hist +157 Fst PCA →new fancy version
- 23:0223:02, 7 June 2015 diff hist +21 Fst PCA →New Fancy Method (sim data)
- 23:0023:00, 7 June 2015 diff hist +11 Fst PCA →New Fancy Method
- 22:5622:56, 7 June 2015 diff hist +153 Fst PCA →New Fancy Method
- 22:1022:10, 7 June 2015 diff hist +91 Fst PCA →New Fancy Method
- 22:0822:08, 7 June 2015 diff hist +98 Fst PCA →New Fancy Method
- 22:0322:03, 7 June 2015 diff hist +156 Fst PCA →New Fancy Method
- 22:0022:00, 7 June 2015 diff hist +1,227 Fst PCA →New Fancy Method
- 21:5721:57, 7 June 2015 diff hist +687 Fst PCA →New Fancy Method
- 21:5421:54, 7 June 2015 diff hist +991 Fst PCA No edit summary
28 May 2015
- 18:4418:44, 28 May 2015 diff hist −2 SFS Estimation →Quick Start
11 May 2015
- 15:3015:30, 11 May 2015 diff hist +12 SFS Estimation →Posterior of the per-site distributions of the sample allele frequency
- 15:2915:29, 11 May 2015 diff hist +243 SFS Estimation →Options
- 15:1115:11, 11 May 2015 diff hist −152 SFS Estimation →-doSaf 1
- 14:4914:49, 11 May 2015 diff hist 0 RealSFS →Brief overview
- 14:4914:49, 11 May 2015 diff hist −1 RealSFS →2dsfs
- 14:3914:39, 11 May 2015 diff hist +21 2d SFS Estimation →Example
- 14:3814:38, 11 May 2015 diff hist −159 2d SFS Estimation →Example
- 14:3814:38, 11 May 2015 diff hist −104 2d SFS Estimation →Example
- 14:3714:37, 11 May 2015 diff hist −805 2d SFS Estimation →Example
- 14:3514:35, 11 May 2015 diff hist +1 MediaWiki:Sidebar No edit summary
- 14:3414:34, 11 May 2015 diff hist +4 MediaWiki:Sidebar No edit summary
- 14:3414:34, 11 May 2015 diff hist −233 2d SFS Estimation No edit summary
- 14:3314:33, 11 May 2015 diff hist +209 RealSFS →Output
- 14:2914:29, 11 May 2015 diff hist −158 RealSFS →2dsfs
- 14:2914:29, 11 May 2015 diff hist −48 RealSFS →1d SFS
- 14:2814:28, 11 May 2015 diff hist −117 RealSFS →Brief overview
- 14:2814:28, 11 May 2015 diff hist −216 RealSFS No edit summary
- 14:2614:26, 11 May 2015 diff hist −78 SFS Estimation →Brief Overview
- 14:2514:25, 11 May 2015 diff hist +30 SFS Estimation →SFS
- 14:2514:25, 11 May 2015 diff hist +50 SFS Estimation →Validation
- 14:2414:24, 11 May 2015 diff hist +80 SFS Estimation →Quick Start
- 14:2314:23, 11 May 2015 diff hist +2 SFS Estimation →Quick Start
- 14:2314:23, 11 May 2015 diff hist +245 SFS Estimation →safv3 comparison
- 14:2014:20, 11 May 2015 diff hist +19 SFS Estimation →-doSaf 2
- 14:2014:20, 11 May 2015 diff hist −11 SFS Estimation →How to plot
- 14:1914:19, 11 May 2015 diff hist −851 SFS Estimation →Format specification of binary .saf file
- 14:1714:17, 11 May 2015 diff hist +1 SFS Estimation →Folded spectra
- 14:1714:17, 11 May 2015 diff hist −16 SFS Estimation →Old wiki page below
- 14:1614:16, 11 May 2015 diff hist −113 SFS Estimation →Quick Start
- 14:1614:16, 11 May 2015 diff hist −8 SFS Estimation →Quick Start
- 14:1514:15, 11 May 2015 diff hist 0 SFS Estimation →New Version
- 14:1514:15, 11 May 2015 diff hist −340 SFS Estimation →Interpretation of the output file
- 14:1414:14, 11 May 2015 diff hist −304 SFS Estimation →Example
- 14:1214:12, 11 May 2015 diff hist 0 Installation No edit summary
- 14:1014:10, 11 May 2015 diff hist +120 Change log No edit summary
- 14:0914:09, 11 May 2015 diff hist 0 MediaWiki:Sitenotice No edit summary
- 10:0910:09, 11 May 2015 diff hist +349 Safv3 →Two population analysis
- 10:0410:04, 11 May 2015 diff hist 0 N File:Safv3to.png No edit summary current
- 10:0010:00, 11 May 2015 diff hist 0 File:Safv3en.png Thorfinn uploaded a new version of "File:Safv3en.png" current
- 09:5809:58, 11 May 2015 diff hist 0 N File:Safv3en.png No edit summary
- 09:5509:55, 11 May 2015 diff hist +54 Safv3 →Two population analysis
- 09:5009:50, 11 May 2015 diff hist +194 Safv3 →Two population analysis
- 09:4609:46, 11 May 2015 diff hist +33 Safv3 →Two population analysis
- 09:4409:44, 11 May 2015 diff hist −645 Safv3 →Two population analysis
- 09:4109:41, 11 May 2015 diff hist +875 Safv3 →Two population analysis
7 May 2015
- 21:1321:13, 7 May 2015 diff hist +113 SFS Estimation →New Version
- 15:3415:34, 7 May 2015 diff hist +1,412 Safv3 →2 population analysis with simulated data
- 14:3414:34, 7 May 2015 diff hist +325 Safv3 →2 population analysis with simulated data
- 13:5313:53, 7 May 2015 diff hist +3,827 Safv3 →Two population analysis
- 13:5013:50, 7 May 2015 diff hist +47 Safv3 →Two population analysis
- 10:5010:50, 7 May 2015 diff hist +100 Safv3 →Two population analysis
- 10:4910:49, 7 May 2015 diff hist +13 Safv3 →One population analysis
- 10:4810:48, 7 May 2015 diff hist +1,477 Safv3 →Two population analysis
- 10:3610:36, 7 May 2015 diff hist +66 Safv3 →One population analysis
- 10:3310:33, 7 May 2015 diff hist +29 Safv3 →One population analysis
- 10:3210:32, 7 May 2015 diff hist +1,057 Safv3 →One population analysis
- 10:2710:27, 7 May 2015 diff hist +574 N Safv3 Created page with "We decided to update the native simple binary double format to a much more intelligent format that allows for random access. The format is described in doc/formats.pdf. This ..."
5 May 2015
- 20:5920:59, 5 May 2015 diff hist +5 MsToGlf →Two populations
- 14:0314:03, 5 May 2015 diff hist +659 SFS Estimation →New Version
- 13:5513:55, 5 May 2015 diff hist +471 SFS Estimation No edit summary
27 April 2015
- 17:0017:00, 27 April 2015 diff hist +72 Vcf →NB
- 16:5316:53, 27 April 2015 diff hist +4 Vcf →Output files
- 16:4716:47, 27 April 2015 diff hist +8,402 N Vcf Created page with "Newer versions of angsd (master 27april2015) supports basic vcf output. This will only include gl and gp tags which can be useful for certain external programs Supply ;-doVc..."
23 April 2015
- 20:2120:21, 23 April 2015 diff hist +1,506 Contamination →Interpretation of output
30 March 2015
- 20:5620:56, 30 March 2015 diff hist −5 Installation →Unix
- 20:5620:56, 30 March 2015 diff hist 0 Installation No edit summary
- 20:4520:45, 30 March 2015 diff hist −20 ANGSD No edit summary
27 March 2015
- 17:3817:38, 27 March 2015 diff hist −5 SnpFilters No edit summary
- 17:2517:25, 27 March 2015 diff hist +163 SnpFilters No edit summary
- 17:2117:21, 27 March 2015 diff hist +1,931 SnpFilters No edit summary
- 17:2017:20, 27 March 2015 diff hist +510 SnpFilters No edit summary
- 17:1217:12, 27 March 2015 diff hist +105 SnpFilters No edit summary
- 17:0717:07, 27 March 2015 diff hist +1 SnpFilters No edit summary
- 17:0717:07, 27 March 2015 diff hist +390 N SnpFilters Created page with "Angsd has different snpfilters. ;* SB1 strand bias1 ;* SB2 strand bias2 ;* SB3 strand bias3 ;* deviation from HWE ;* Wilcox rank sum test for position in read The 3 stran..."
- 17:0117:01, 27 March 2015 diff hist +26 MediaWiki:Sidebar No edit summary
- 13:1713:17, 27 March 2015 diff hist +2 Mismatch No edit summary
- 13:1713:17, 27 March 2015 diff hist +546 Mismatch No edit summary
- 13:1413:14, 27 March 2015 diff hist +157 N Mismatch Created page with "Angsd can output mismatch from the reference given: ;Distance from be beginning of the read (posi) ;Distance from the end of the read (isop) ;Strand ;Qscore"
- 13:1013:10, 27 March 2015 diff hist +22 MediaWiki:Sidebar No edit summary
17 March 2015
- 13:0513:05, 17 March 2015 diff hist 0 Beagle input →Example
6 March 2015
- 17:0017:00, 6 March 2015 diff hist −8 Input →VCF files
5 March 2015
- 17:3817:38, 5 March 2015 diff hist −115 MediaWiki:Sitenotice No edit summary
- 17:3517:35, 5 March 2015 diff hist −8 Thorfinn No edit summary
- 17:2817:28, 5 March 2015 diff hist +61 MediaWiki:Sitenotice No edit summary
- 17:2817:28, 5 March 2015 diff hist +54 MediaWiki:Sitenotice No edit summary
28 February 2015
- 00:4900:49, 28 February 2015 diff hist −39 Contamination No edit summary
26 February 2015
- 17:0717:07, 26 February 2015 diff hist +133 Input No edit summary
- 17:0617:06, 26 February 2015 diff hist +5 Input No edit summary
- 17:0517:05, 26 February 2015 diff hist −7 Bugs No edit summary current
- 17:0517:05, 26 February 2015 diff hist −20 Bugs No edit summary
- 16:4016:40, 26 February 2015 diff hist −5 Installation →Unix
- 16:3616:36, 26 February 2015 diff hist −21 Installation →Install CRAM version
- 16:3616:36, 26 February 2015 diff hist −107 Installation →Unix
- 16:3516:35, 26 February 2015 diff hist +19 Installation →Download
- 16:1716:17, 26 February 2015 diff hist +15 MediaWiki:Sitenotice No edit summary
- 16:1616:16, 26 February 2015 diff hist 0 Change log No edit summary
- 16:1616:16, 26 February 2015 diff hist +11 Change log No edit summary
- 15:5915:59, 26 February 2015 diff hist +60 Change log No edit summary
- 15:5815:58, 26 February 2015 diff hist +60 Change log No edit summary
- 15:5715:57, 26 February 2015 diff hist −51 MediaWiki:Sitenotice No edit summary
24 February 2015
- 23:2923:29, 24 February 2015 diff hist +242 ANGSD No edit summary
- 23:2623:26, 24 February 2015 diff hist +265 Installation →Install
- 23:2323:23, 24 February 2015 diff hist +56 Installation →Download
- 23:1623:16, 24 February 2015 diff hist +72 MediaWiki:Sitenotice No edit summary
21 February 2015
- 12:1812:18, 21 February 2015 diff hist 0 MediaWiki:Sitenotice No edit summary
- 12:1612:16, 21 February 2015 diff hist 0 Installation No edit summary