User contributions for Albrecht

21 June 2012

• 10:3410:34, 21 June 2012 diff hist +1,043‎ Association ‎ →‎Association
• 09:2309:23, 21 June 2012 diff hist +242‎ Beagle input ‎ →‎output
• 09:2109:21, 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..."
• 09:1209:12, 21 June 2012 diff hist +32‎ Association ‎ →‎Association
• 09:1109:11, 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
• 09:1109:11, 21 June 2012 diff hist −1‎ Association ‎ →‎Score statistic
• 09:1009:10, 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
• 09:1009:10, 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
• 09:0909:09, 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

• 14:2114:21, 19 June 2012 diff hist +66‎ Input ‎ →‎optional arguments
• 12:4312:43, 19 June 2012 diff hist +1‎ ANGSD ‎ →‎Overview of input and intermediary data
• 12:3812:38, 19 June 2012 diff hist +30‎ ANGSD ‎ →‎Synopsis
• 10:0310:03, 19 June 2012 diff hist +10‎ MediaWiki:Sidebar ‎No edit summary
• 09:5409:54, 19 June 2012 diff hist +200‎ Genotype Likelihoods ‎ →‎Genotype likelihoods from alignments

18 June 2012

• 19:4719:47, 18 June 2012 diff hist 0‎ Genotype Likelihoods ‎ →‎Genotype likelihoods from alignments
• 19:0519:05, 18 June 2012 diff hist +178‎ Genotype Likelihoods ‎No edit summary
• 18:5518:55, 18 June 2012 diff hist −3‎ MediaWiki:Sidebar ‎No edit summary
• 18:5318:53, 18 June 2012 diff hist +1,262‎ Allele Counts ‎ →‎dumping counts
• 18:3918:39, 18 June 2012 diff hist −1‎ Allele Frequencies ‎ →‎Allele Frequency estimation
• 18:3518:35, 18 June 2012 diff hist +240‎ ANGSD ‎ →‎Analysis from genotype probabilities
• 18:0618:06, 18 June 2012 diff hist +14‎ Input ‎ →‎glfv3
• 18:0418:04, 18 June 2012 diff hist +54‎ ANGSD ‎ →‎About
• 18:0318:03, 18 June 2012 diff hist −463‎ ANGSD ‎ →‎Commands
• 17:2317:23, 18 June 2012 diff hist −10‎ Allele Frequencies ‎No edit summary
• 17:2117:21, 18 June 2012 diff hist −12‎ Input ‎No edit summary
• 17:1117:11, 18 June 2012 diff hist −79‎ ANGSD ‎ →‎Wish list
• 17:0817:08, 18 June 2012 diff hist +86‎ Change log ‎ →‎Version notes
• 17:0817:08, 18 June 2012 diff hist −649‎ ANGSD ‎ →‎Possible Bugs
• 17:0717:07, 18 June 2012 diff hist −1,934‎ ANGSD ‎ →‎Version notes
• 17:0717:07, 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..."
• 17:0617:06, 18 June 2012 diff hist +26‎ MediaWiki:Sidebar ‎No edit summary
• 17:0617:06, 18 June 2012 diff hist +85‎ ANGSD ‎ →‎Possible Bugs
• 17:0517:05, 18 June 2012 diff hist −185‎ ANGSD ‎ →‎Example for getting the depths with bamfiles
• 17:0417:04, 18 June 2012 diff hist −322‎ ANGSD ‎ →‎sfstools
• 17:0417:04, 18 June 2012 diff hist −1,530‎ ANGSD ‎ →‎Run Examples
• 17:0417:04, 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..."
• 17:0417:04, 18 June 2012 diff hist +36‎ MediaWiki:Sidebar ‎No edit summary
• 17:0317:03, 18 June 2012 diff hist −708‎ ANGSD ‎ →‎All options
• 16:3416:34, 18 June 2012 diff hist −97‎ ANGSD ‎ →‎Association study
• 16:2916:29, 18 June 2012 diff hist +97‎ Association ‎No edit summary
• 16:2416:24, 18 June 2012 diff hist −726‎ ANGSD ‎ →‎Input sequencing data
• 16:2416:24, 18 June 2012 diff hist +447‎ Input ‎ →‎genotype likelihood files
• 16:2216:22, 18 June 2012 diff hist −821‎ ANGSD ‎ →‎Output data
• 16:2216:22, 18 June 2012 diff hist −973‎ ANGSD ‎ →‎Association
• 15:3915:39, 18 June 2012 diff hist +983‎ Association ‎No edit summary
• 15:2915:29, 18 June 2012 diff hist +822‎ Allele Frequencies ‎ →‎Allele Frequency estimation
• 15:2715:27, 18 June 2012 diff hist −10‎ ANGSD ‎ →‎Methods
• 15:2715:27, 18 June 2012 diff hist −74‎ ANGSD ‎ →‎HWE and Inbreeding estimates
• 15:2715:27, 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
• 15:2615:26, 18 June 2012 diff hist +72‎ N HWE and Inbreeding estimates ‎ Created page with "==HWE and Inbreeding estimates== For method details see here"