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
Jump to navigation
Jump to search
10 October 2012
- 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
19 June 2012
- 15:2115:21, 19 June 2012 diff hist +66 Input →optional arguments
- 13:4313:43, 19 June 2012 diff hist +1 ANGSD →Overview of input and intermediary data
- 13:3813:38, 19 June 2012 diff hist +30 ANGSD →Synopsis
- 11:0311:03, 19 June 2012 diff hist +10 MediaWiki:Sidebar No edit summary
- 10:5410:54, 19 June 2012 diff hist +200 Genotype Likelihoods →Genotype likelihoods from alignments
18 June 2012
- 20:4720:47, 18 June 2012 diff hist 0 Genotype Likelihoods →Genotype likelihoods from alignments
- 20:0520:05, 18 June 2012 diff hist +178 Genotype Likelihoods No edit summary
- 19:5519:55, 18 June 2012 diff hist −3 MediaWiki:Sidebar No edit summary
- 19:5319:53, 18 June 2012 diff hist +1,262 Allele Counts →dumping counts
- 19:3919:39, 18 June 2012 diff hist −1 Allele Frequencies →Allele Frequency estimation
- 19:3519:35, 18 June 2012 diff hist +240 ANGSD →Analysis from genotype probabilities
- 19:0619:06, 18 June 2012 diff hist +14 Input →glfv3
- 19:0419:04, 18 June 2012 diff hist +54 ANGSD →About
- 19:0319:03, 18 June 2012 diff hist −463 ANGSD →Commands
- 18:2318:23, 18 June 2012 diff hist −10 Allele Frequencies No edit summary
- 18:2118:21, 18 June 2012 diff hist −12 Input No edit summary
- 18:1118:11, 18 June 2012 diff hist −79 ANGSD →Wish list
- 18:0818:08, 18 June 2012 diff hist +86 Change log →Version notes
- 18:0818:08, 18 June 2012 diff hist −649 ANGSD →Possible Bugs
- 18:0718:07, 18 June 2012 diff hist −1,934 ANGSD →Version notes
- 18:0718:07, 18 June 2012 diff hist +1,932 N Change log Created page with "=Version notes= * 0.16 Is now bundled with SAMtools-0.1.17 and the mpileup (and friends) command be used for passing data to dirty. * 0.17 added extra options -minInd and -min..."
- 18:0618:06, 18 June 2012 diff hist +26 MediaWiki:Sidebar No edit summary
- 18:0618:06, 18 June 2012 diff hist +85 ANGSD →Possible Bugs
- 18:0518:05, 18 June 2012 diff hist −185 ANGSD →Example for getting the depths with bamfiles
- 18:0418:04, 18 June 2012 diff hist −322 ANGSD →sfstools
- 18:0418:04, 18 June 2012 diff hist −1,530 ANGSD →Run Examples
- 18:0418:04, 18 June 2012 diff hist +1,528 N Misc example Created page with "=Run Examples= ==Using glfv3== <code lang="sh"> ../dirty -samglf ceu.glf.list -outfiles test.glf -doMaf 2 -fai numSort.Fai -nLines 50000 -chunkSize 500 -nThreads 16 </code..."
- 18:0418:04, 18 June 2012 diff hist +36 MediaWiki:Sidebar No edit summary
- 18:0318:03, 18 June 2012 diff hist −708 ANGSD →All options
- 17:3417:34, 18 June 2012 diff hist −97 ANGSD →Association study
- 17:2917:29, 18 June 2012 diff hist +97 Association No edit summary
- 17:2417:24, 18 June 2012 diff hist −726 ANGSD →Input sequencing data
- 17:2417:24, 18 June 2012 diff hist +447 Input →genotype likelihood files
- 17:2217:22, 18 June 2012 diff hist −821 ANGSD →Output data
- 17:2217:22, 18 June 2012 diff hist −973 ANGSD →Association
- 16:3916:39, 18 June 2012 diff hist +983 Association No edit summary
- 16:2916:29, 18 June 2012 diff hist +822 Allele Frequencies →Allele Frequency estimation
- 16:2716:27, 18 June 2012 diff hist −10 ANGSD →Methods
- 16:2716:27, 18 June 2012 diff hist −74 ANGSD →HWE and Inbreeding estimates
- 16:2716:27, 18 June 2012 diff hist +3,624 N Inbreed Created page with "Definition <math> \begin{align} p(AA)&=P_A^2+p_Ap_aF \\ p(Aa)&=2P_Ap_a-2p_Ap_aF \end{align} </math> ;n: total number of individuals ;X: all sequencing data ;f: allele frequ..." current
- 16:2616:26, 18 June 2012 diff hist +72 N HWE and Inbreeding estimates Created page with "==HWE and Inbreeding estimates== For method details see here"