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 Albrecht
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22 March 2013
- 19:1019:10, 22 March 2013 diff hist +130 MediaWiki:Sidebar No edit summary
- 16:2716:27, 22 March 2013 diff hist −33 ANGSD No edit summary
27 February 2013
- 12:1112:11, 27 February 2013 diff hist −72 Base quality →options
- 12:1012:10, 27 February 2013 diff hist −67 Error estimation →additional options
- 12:1012:10, 27 February 2013 diff hist −72 Allele Counts →options
- 12:1012:10, 27 February 2013 diff hist −72 Genotype Likelihoods →options
- 12:0812:08, 27 February 2013 diff hist −71 Genotype Likelihoods →options
- 12:0812:08, 27 February 2013 diff hist −72 Genotype Likelihoods →options
13 February 2013
- 11:5011:50, 13 February 2013 diff hist +278 Error estimation →example
12 February 2013
- 18:1218:12, 12 February 2013 diff hist −17 Error estimation →Error estimation using an outgroup and an error free individual
- 18:1218:12, 12 February 2013 diff hist +116 Error estimation →Error estimation using an outgroup and an error free individual
- 18:0618:06, 12 February 2013 diff hist +719 Error estimation →Error estimation using an outgroup and an error free individual
- 17:5317:53, 12 February 2013 diff hist −14 Error estimation method No edit summary current
- 17:5217:52, 12 February 2013 diff hist +1,483 N Error estimation method Created page with " The estimated rates can roughly be intrepreted as relative error rates. That is excess of errors in your sample compare to the error in the perfect indviduals. The idea is th..."
29 January 2013
- 19:1719:17, 29 January 2013 diff hist +1 Depth →Output
17 January 2013
- 20:2320:23, 17 January 2013 diff hist +16 Input →arguments
14 January 2013
4 December 2012
- 19:1019:10, 4 December 2012 diff hist −1,035 Bugs No edit summary
- 18:5818:58, 4 December 2012 diff hist +17 Bugs No edit summary
23 October 2012
- 21:1721:17, 23 October 2012 diff hist 0 MediaWiki:Sidebar No edit summary
- 21:1021:10, 23 October 2012 diff hist −2 MediaWiki:Sidebar No edit summary
- 20:4420:44, 23 October 2012 diff hist −2,321 Change log →Version notes
- 20:3620:36, 23 October 2012 diff hist 0 Citing angsd →Maf estimation from counts of alleles
- 20:3620:36, 23 October 2012 diff hist +2 Citing angsd →Maf estimation from counts of alleles
- 19:0919:09, 23 October 2012 diff hist +29 MediaWiki:Sidebar No edit summary
- 19:0819:08, 23 October 2012 diff hist +33 MediaWiki:Sidebar No edit summary
16 October 2012
- 15:5515:55, 16 October 2012 diff hist 0 MediaWiki:Sidebar No edit summary
- 15:5015:50, 16 October 2012 diff hist +4 Citing angsd →Maf estimation from counts of alleles
- 15:5015:50, 16 October 2012 diff hist −2 Citing angsd →Maf estimation from counts of alleles
- 15:4815:48, 16 October 2012 diff hist +7 MediaWiki:Sidebar No edit summary
- 15:4415:44, 16 October 2012 diff hist −13 Error estimation →example
- 15:4115:41, 16 October 2012 diff hist −380 Installation →Misc folder
10 October 2012
- 21:0021:00, 10 October 2012 diff hist −29 Major Minor →From genotype likelihood data
- 21:0021:00, 10 October 2012 diff hist −1 Major Minor →From alignment data
- 20:5920:59, 10 October 2012 diff hist +17 Major Minor →From genotype probability data
- 20:1020:10, 10 October 2012 diff hist +9 MediaWiki:Sidebar No edit summary
- 20:1020:10, 10 October 2012 diff hist +1 Genotype calling →example
- 20:0920:09, 10 October 2012 diff hist +1,248 Genotype calling →Genotype calling
- 18:3818:38, 10 October 2012 diff hist −143 Genotype calling →Genotype calling
- 16:4916:49, 10 October 2012 diff hist +63 Association →example
- 15:1815:18, 10 October 2012 diff hist +20 Association →example
- 15:1615:16, 10 October 2012 diff hist +40 Association →example
- 15:0215:02, 10 October 2012 diff hist +346 Association →Score statistic
- 15:0015:00, 10 October 2012 diff hist +143 Association →Case control association using allele frequencies
- 14:5014:50, 10 October 2012 diff hist −6 Association No edit summary
- 14:5014:50, 10 October 2012 diff hist +95 Association →Case control association using allele frequencies
- 14:2414:24, 10 October 2012 diff hist +18 MediaWiki:Sidebar No edit summary
- 14:2414:24, 10 October 2012 diff hist +9 MediaWiki:Sidebar No edit summary
- 11:2411:24, 10 October 2012 diff hist +228 Input →genotype probability files
28 September 2012
- 16:2616:26, 28 September 2012 diff hist +1 Input →optional arguments
24 September 2012
- 17:3117:31, 24 September 2012 diff hist −16 Installation →Download
- 15:2915:29, 24 September 2012 diff hist −53 Filters →Selected Sites
- 13:5513:55, 24 September 2012 diff hist +123 Citing angsd →Methods
- 13:3513:35, 24 September 2012 diff hist +260 N Gatk Created page with "McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce ..."
- 13:3413:34, 24 September 2012 diff hist +80 Citing angsd No edit summary
- 13:3213:32, 24 September 2012 diff hist +175 N SoapSNP Created page with "Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. SNP detection for massively parallel whole-genome resequencing. Genome Res. 2009 Jun;19(6):1124-32. Epub 2009 May 6." current
- 13:2813:28, 24 September 2012 diff hist −7 Citing angsd No edit summary
- 13:2813:28, 24 September 2012 diff hist −179 Skotte Blanked the page current
- 13:2713:27, 24 September 2012 diff hist +179 N Skotte2012 Created page with "Line Skotte, Thorfinn Sand Korneliussen, Anders Albrechtsen. Association testing for next-generation sequencing data using score statistics. Genet Epidemiol. 2012 Jul;36(5):43..."
- 13:2513:25, 24 September 2012 diff hist −221 SuYeon Redirected page to Kim2011 current
- 13:2513:25, 24 September 2012 diff hist +242 N Kim2011 Created page with "Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witte D, et al., 2011. Estimation of allele frequency and association mappin..."
- 13:0713:07, 24 September 2012 diff hist +26 Filters No edit summary
- 13:0613:06, 24 September 2012 diff hist +24 Filters No edit summary
- 13:0513:05, 24 September 2012 diff hist +72 Filters No edit summary
21 September 2012
- 15:4715:47, 21 September 2012 diff hist +376 N Citing angsd Created page with "Currently there is not publication for angsd. However, many of the method implimented here are published. **Methods** allele estimation from genotype likelihoods ;- doMaf ..."
- 15:4315:43, 21 September 2012 diff hist +29 MediaWiki:Sidebar No edit summary
- 15:2715:27, 21 September 2012 diff hist +1,787 SNP calling No edit summary
- 15:1015:10, 21 September 2012 diff hist −36 MediaWiki:Sidebar No edit summary
20 September 2012
- 15:5015:50, 20 September 2012 diff hist +392 Error estimation No edit summary
19 September 2012
- 18:1518:15, 19 September 2012 diff hist +281 Genotype Likelihoods →output genotype likelihoods
- 18:0318:03, 19 September 2012 diff hist +2,006 Genotype Likelihoods →output genotype likelihoods
- 18:0018:00, 19 September 2012 diff hist +1 Genotype Likelihoods No edit summary
- 17:4817:48, 19 September 2012 diff hist +915 Genotype Likelihoods No edit summary
- 17:3517:35, 19 September 2012 diff hist +36 Genotype Likelihoods →Genotype likelihoods from alignments
- 17:2317:23, 19 September 2012 diff hist +296 Base quality No edit summary
- 17:2217:22, 19 September 2012 diff hist +15 Base quality →Example
- 17:2117:21, 19 September 2012 diff hist −21 Base quality No edit summary
- 17:2017:20, 19 September 2012 diff hist +353 Base quality No edit summary
- 17:1117:11, 19 September 2012 diff hist +196 N Base quality Created page with "=Base quality counts= Counts the number of bases for each quality. ==Example== Print the individuals depth from bam files <pre> ./angsd -out out -doCounts 1 -doQsDist 1 -ba..."
- 17:0317:03, 19 September 2012 diff hist +42 Allele Counts →options
- 16:5816:58, 19 September 2012 diff hist +44 MediaWiki:Sidebar No edit summary
- 16:5616:56, 19 September 2012 diff hist +106 Allele Counts →options
- 16:5316:53, 19 September 2012 diff hist +251 Allele Counts No edit summary
17 September 2012
- 16:1516:15, 17 September 2012 diff hist +6 Genotype Likelihoods →soapSNP
- 16:0416:04, 17 September 2012 diff hist −34 Genotype Likelihoods →Genotype likelihoods from alignments
16 July 2012
- 18:3918:39, 16 July 2012 diff hist +184 Genotype Likelihoods →Samtools
- 18:1618:16, 16 July 2012 diff hist −70 Genotype Likelihoods →soapSNP
22 June 2012
- 16:0016:00, 22 June 2012 diff hist +64 Genotype Likelihoods →Genotype likelihoods from alignments
21 June 2012
- 16:5416:54, 21 June 2012 diff hist +97 Genotype Likelihoods →Genotype likelihoods from alignments
- 11:4511:45, 21 June 2012 diff hist +30 Association →Score statistic
- 11:4211:42, 21 June 2012 diff hist −97 Association →Association study
- 11:3411:34, 21 June 2012 diff hist +1,043 Association →Association
- 10:2310:23, 21 June 2012 diff hist +242 Beagle input →output
- 10:2110:21, 21 June 2012 diff hist +1,687 N Beagle input Created page with "Beagle haplotype imputation and be performed directly on genotype likelhoods. To generate beagle input file use ; -doGlf 2 In order to make this file the major and minor all..."
- 10:1210:12, 21 June 2012 diff hist +32 Association →Association
- 10:1110:11, 21 June 2012 diff hist +271 N Example of a covariate file Created page with "1 0 0 1 <br> 1 0.1 0 0 <br> 2 0 1 0 <br> 2 0 1 0 <br> 2 0.1 0 1 <br> 1 0 0 1 <br> 1 0.3 0 0 <br> 2 0 0 0 <br> 1 0 0 0 <br> 2 0.2 0 1 <br> 1 0 1 0 <br> 1 0 0 0 <br> 1 0.1 0 0 <..." current
- 10:1110:11, 21 June 2012 diff hist −1 Association →Score statistic
- 10:1010:10, 21 June 2012 diff hist +271 N Example of a covariance file Created page with "1 0 0 1 <br> 1 0.1 0 0 <br> 2 0 1 0 <br> 2 0 1 0 <br> 2 0.1 0 1 <br> 1 0 0 1 <br> 1 0.3 0 0 <br> 2 0 0 0 <br> 1 0 0 0 <br> 2 0.2 0 1 <br> 1 0 1 0 <br> 1 0 0 0 <br> 1 0.1 0 0 <..." current
- 10:1010:10, 21 June 2012 diff hist +364 N Example of a quantitative phenotype file Created page with "-999<br> 2.06164722761138<br> -0.091935218675602<br> -0.287527686061831<br> -999<br> -999<br> -1.20996664036026<br> 0.0188541092307412<br> -2.1122713873334<br> -999<br> -1.329..." current
- 10:0910:09, 21 June 2012 diff hist +98 N Example of cases control phenotype file Created page with "1<br> 0<br> 0<br> 0<br> 1<br> 1<br> 1<br> 1<br> 0<br> -999<br> 1<br> 0<br> 0<br> 0<br> 0<br> 1<br>" current