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
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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