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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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"
- 16:2616:26, 18 June 2012 diff hist −21 ANGSD →Heterozygosity
- 16:2616:26, 18 June 2012 diff hist −1,603 ANGSD →Full example for simulating nextgen data and estimating SFS (somewhat deprecated should use sfstools now)
- 16:2516:25, 18 June 2012 diff hist +1,603 SFS Estimation No edit summary
- 16:2516:25, 18 June 2012 diff hist −686 ANGSD →Download and Installation
- 16:2416:24, 18 June 2012 diff hist +380 Installation No edit summary
- 16:2116:21, 18 June 2012 diff hist −2,753 ANGSD →Association
- 16:2116:21, 18 June 2012 diff hist +2,751 N Association Created page with "==Association== Association can be performed using two approaches. One based on testing differences in allele frequencies between cases and control while the other is based o..."
- 16:2116:21, 18 June 2012 diff hist −97 MediaWiki:Sidebar No edit summary
- 16:2016:20, 18 June 2012 diff hist +97 MediaWiki:Sidebar No edit summary