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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18 June 2012
- 16:1916:19, 18 June 2012 diff hist +29 N Covariance matrix for PCA Created page with "==Covariance matrix for PCA==" current
- 16:1916:19, 18 June 2012 diff hist −31 ANGSD →Covariance matrix for PCA
- 16:1816:18, 18 June 2012 diff hist +745 N SNP calling Created page with "==SNP Calling== ===Likelihood ratio test=== supply -doSNP 1 Then the MAF estimate(s) given by -doMaf INT, will be used for a like ratio test <pre> chromo position ma..."
- 16:1816:18, 18 June 2012 diff hist −747 ANGSD →SNP Calling
- 16:1816:18, 18 June 2012 diff hist +27 MediaWiki:Sidebar No edit summary
- 16:1816:18, 18 June 2012 diff hist +125 N Genotype Likelihoods Created page with "==Genotype likelihoods from alignments== ===Kim et al.=== Citation Citation ===Samtools=== ===GATK==="
- 16:1716:17, 18 June 2012 diff hist −127 ANGSD →Genotype likelihoods from alignments
- 16:1716:17, 18 June 2012 diff hist −780 ANGSD →Genotype calling
- 16:1716:17, 18 June 2012 diff hist +778 N Genotype calling Created page with "==Genotype calling== output file .geno -doGeno 1, print out major minor -doGeno 2, print the called genotype under HWE (suyeon maf prior method) -doGeno 4, print out the g..."
- 16:1716:17, 18 June 2012 diff hist +17 MediaWiki:Sidebar No edit summary
- 16:1616:16, 18 June 2012 diff hist +20 MediaWiki:Sidebar No edit summary
- 16:1516:15, 18 June 2012 diff hist +2 MediaWiki:Sidebar No edit summary
- 16:1516:15, 18 June 2012 diff hist −238 ANGSD →dumping counts
- 16:1516:15, 18 June 2012 diff hist +236 N Allele Counts Created page with "==dumping counts== -dumpCounts 1, print overall depth in the .pos file -dumpCounts 2, 1) plus .counts with overall sample depth, each line nInd long -dumpCounts 3,..."
- 16:1416:14, 18 June 2012 diff hist +44 MediaWiki:Sidebar No edit summary
- 16:1416:14, 18 June 2012 diff hist −86 ANGSD →Error estimation
- 16:1416:14, 18 June 2012 diff hist +84 N Error estimation Created page with "==Error estimation== ===Kim et al.=== Citation ===Using an outgroup==="
- 16:1316:13, 18 June 2012 diff hist −336 ANGSD →realSFS
- 16:1316:13, 18 June 2012 diff hist +334 N SFS Estimation Created page with "==realSFS== From version 0.20 we can now estimate the joint likelihood of being in frequency j. From version 0.24 the tajima is being estimated -realSFS 1 an sfs file will ..."
- 15:5515:55, 18 June 2012 diff hist +2 Allele Frequencies →Example
- 15:5515:55, 18 June 2012 diff hist +174 Allele Frequencies →Estimator from genotype probabilities
- 15:5315:53, 18 June 2012 diff hist +397 Allele Frequencies →Allele frequencies from genotype likelihoods
- 14:4414:44, 18 June 2012 diff hist +91 Allele Frequencies →Estimator from sequencing data
- 13:2713:27, 18 June 2012 diff hist +1 Allele Frequencies →ML estimator with known minor
- 13:2713:27, 18 June 2012 diff hist +2 Allele Frequencies →Allele Frequency estimation
- 13:2613:26, 18 June 2012 diff hist +305 Allele Frequencies No edit summary
- 12:1512:15, 18 June 2012 diff hist +1,576 Allele Frequencies No edit summary
15 June 2012
- 11:1411:14, 15 June 2012 diff hist +242 N SuYeon 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..."
- 11:1411:14, 15 June 2012 diff hist +4 Allele Frequencies No edit summary
- 11:1311:13, 15 June 2012 diff hist +229 Allele Frequencies No edit summary
14 June 2012
- 22:0222:02, 14 June 2012 diff hist +240 N Allele Frequencies Created page with "==Allele Frequency estimation== -doMaf INT INT=1 bfgs known minor INT=2 EM known minor INT=4 BFGS unknown minor INT=8 EM unknown minor ===Phat estimator=== ===ML est..."
- 21:5921:59, 14 June 2012 diff hist −242 ANGSD →Allele Frequency estimation
- 21:5921:59, 14 June 2012 diff hist −460 ANGSD →Inferring Major and Minor alleles
- 21:4121:41, 14 June 2012 diff hist +1,183 N Majorminor Created page with "Assuming that the considered site is diallelic, we infer those two alleles using the genotype likelihoods. Let <math>\{M,m\}</math> denote the two possible alleles at the dial..." current
- 21:4121:41, 14 June 2012 diff hist +179 N Skotte 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..."
- 21:4021:40, 14 June 2012 diff hist +256 N Li2010 Created page with "Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, et al., 2010. Resequencing of 200 human exomes identifies a..." current
- 21:3921:39, 14 June 2012 diff hist +1,015 Major Minor No edit summary
- 20:2320:23, 14 June 2012 diff hist −3 Input →optional arguments
- 20:2320:23, 14 June 2012 diff hist +179 Input →optional arguments
- 20:2120:21, 14 June 2012 diff hist +181 Input →obtional arguments
- 19:4519:45, 14 June 2012 diff hist +569 Input →bam files
- 19:2119:21, 14 June 2012 diff hist −3 Input →options
- 19:2119:21, 14 June 2012 diff hist −6 Input →Mapped sequence file
- 19:2119:21, 14 June 2012 diff hist +830 Input No edit summary
- 19:1619:16, 14 June 2012 diff hist −17 Input →Mapped sequence file
- 19:0219:02, 14 June 2012 diff hist −4 Input →example
- 18:5718:57, 14 June 2012 diff hist +285 N Installation Created page with "=Download= The source code is avaible as a tarball and be download here [http://popgen.dk/software/download/angsd/angsd0.3.tar.gz] =Install= Unpack the tarball ===Unix=== Th..."
11 June 2012
- 17:0917:09, 11 June 2012 diff hist +1 Input →example
- 16:5216:52, 11 June 2012 diff hist +988 Input →beagle format
- 12:2912:29, 11 June 2012 diff hist +26 MediaWiki:Sidebar No edit summary
- 12:2812:28, 11 June 2012 diff hist −120 MediaWiki:Sidebar No edit summary
- 12:2312:23, 11 June 2012 diff hist −10 MediaWiki:Sidebar No edit summary
- 12:2312:23, 11 June 2012 diff hist +11 MediaWiki:Sidebar No edit summary
- 12:2312:23, 11 June 2012 diff hist −16 MediaWiki:Sidebar No edit summary
- 12:2212:22, 11 June 2012 diff hist +257 N Input Created page with "ANSGD currently supports various mapped data, genotype likelihood formats and imputed genotype probability files =Mapped sequence file= ==bam files== ==soap files== =geno..."
- 12:1912:19, 11 June 2012 diff hist −14 ANGSD →Input data
- 12:1612:16, 11 June 2012 diff hist −633 ANGSD No edit summary
- 12:1412:14, 11 June 2012 diff hist +16 ANGSD No edit summary
- 11:5911:59, 11 June 2012 diff hist +161 ANGSD →About
- 11:5511:55, 11 June 2012 diff hist +30 ANGSD →overview
- 11:5311:53, 11 June 2012 diff hist +246 ANGSD →About
- 11:5011:50, 11 June 2012 diff hist +17 ANGSD →About
- 11:4811:48, 11 June 2012 diff hist +28 ANGSD →About
- 11:4711:47, 11 June 2012 diff hist +30 MediaWiki:Sitenotice No edit summary
- 11:4511:45, 11 June 2012 diff hist 0 File:Banner.png Albrecht uploaded a new version of "File:Banner.png" current
- 11:4211:42, 11 June 2012 diff hist −29 MediaWiki:Sitenotice No edit summary
- 11:4111:41, 11 June 2012 diff hist +28 MediaWiki:Sitenotice No edit summary
- 11:4011:40, 11 June 2012 diff hist 0 File:Banner.png Albrecht uploaded a new version of "File:Banner.png"
- 11:3311:33, 11 June 2012 diff hist −27 ANGSD No edit summary
- 11:3311:33, 11 June 2012 diff hist 0 N File:Banner.png No edit summary
- 11:3211:32, 11 June 2012 diff hist 0 MediaWiki:Sitenotice No edit summary
- 11:3211:32, 11 June 2012 diff hist +21 N MediaWiki:Sitenotice Created page with " Image:banner.gif"
- 11:3111:31, 11 June 2012 diff hist +29 ANGSD No edit summary
29 May 2012
- 23:0323:03, 29 May 2012 diff hist −127 ANGSD →overview
- 23:0323:03, 29 May 2012 diff hist +6 ANGSD →About
- 23:0123:01, 29 May 2012 diff hist +330 ANGSD →overview
- 22:2422:24, 29 May 2012 diff hist −49 ANGSD →genotype probabilities
- 22:2422:24, 29 May 2012 diff hist −89 ANGSD →genotype likelihoods
- 22:2322:23, 29 May 2012 diff hist −52 ANGSD →sequencing data
- 21:4721:47, 29 May 2012 diff hist +587 N Temp Created page with "<classdiagram> [sequence data]->[genotype;likelihoods] [bam files{bg:orange}]->[sequence data] [SOAP files{bg:orange}]->[sequence data] [sequence data]->[phat estimates;er..." current
- 21:4121:41, 29 May 2012 diff hist +233 ANGSD →genotype probabilities
- 21:3821:38, 29 May 2012 diff hist −21 ANGSD →About
- 21:3721:37, 29 May 2012 diff hist +344 ANGSD →genotype likelihoods
- 21:2921:29, 29 May 2012 diff hist +223 ANGSD →sequencing data
- 21:1721:17, 29 May 2012 diff hist +180 ANGSD →About
- 21:1721:17, 29 May 2012 diff hist +35 ANGSD No edit summary
- 20:2420:24, 29 May 2012 diff hist 0 ANGSD →about
- 20:2420:24, 29 May 2012 diff hist −422 ANGSD No edit summary
- 20:2220:22, 29 May 2012 diff hist +19 N Main Page Albrecht moved page Main Page to ANGSD current
- 20:2220:22, 29 May 2012 diff hist 0 m ANGSD Albrecht moved page Main Page to ANGSD
- 20:1620:16, 29 May 2012 diff hist +29 ANGSD No edit summary
- 20:1020:10, 29 May 2012 diff hist 0 N File:AngsdLogo.png No edit summary current
- 18:2018:20, 29 May 2012 diff hist +26 ANGSD No edit summary
- 17:5517:55, 29 May 2012 diff hist +4 MediaWiki:Mainpage No edit summary current
- 17:5417:54, 29 May 2012 diff hist +5 N MediaWiki:Mainpage Created page with "ANGSD"
- 17:4817:48, 29 May 2012 diff hist −399 MediaWiki:Sidebar No edit summary
- 17:4517:45, 29 May 2012 diff hist −288 MediaWiki:Sidebar No edit summary
- 17:4317:43, 29 May 2012 diff hist +1,617 N MediaWiki:Sidebar Created page with "* Pages ** http://130.225.210.106/dirtywiki/index.php/Main_Page#Download|dirty ** http://130.225.210.106/dirtywiki/index.php/Main_Page#Installation|Installation ** http://130...."
- 17:4217:42, 29 May 2012 diff hist +16,749 ANGSD No edit summary
- 17:3717:37, 29 May 2012 diff hist −34 ANGSD No edit summary