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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6 March 2014
- 13:1513:15, 6 March 2014 diff hist +347 SFS Estimation →Options
- 12:2712:27, 6 March 2014 diff hist +148 SFS Estimation →Options
- 12:2612:26, 6 March 2014 diff hist +52 SFS Estimation →Posterior per-site distributions of the sample allele frequency
- 12:2312:23, 6 March 2014 diff hist +13 SFS Estimation →Interpretation of output file
- 12:2312:23, 6 March 2014 diff hist +47 SFS Estimation →Interpretation of output file
- 12:2012:20, 6 March 2014 diff hist −3 SFS Estimation →Example
- 12:2012:20, 6 March 2014 diff hist +155 SFS Estimation →Example
- 12:1812:18, 6 March 2014 diff hist +188 SFS Estimation →Brief Overview
- 12:1712:17, 6 March 2014 diff hist −64 SFS Estimation →Example
- 12:1612:16, 6 March 2014 diff hist +98 SFS Estimation →Example
- 12:1512:15, 6 March 2014 diff hist −1 SFS Estimation →Example
- 12:1112:11, 6 March 2014 diff hist +1 SFS Estimation →How to plot
- 12:1012:10, 6 March 2014 diff hist +43 SFS Estimation →How to plot
- 12:0912:09, 6 March 2014 diff hist −2,070 SFS Estimation →Theory
- 12:0912:09, 6 March 2014 diff hist −11 RealSFSmethod →Theory
- 12:0812:08, 6 March 2014 diff hist +2,068 N RealSFSmethod Created page with "=Theory= <pre> We will try to elaborate on the theory behind the methods. Below is only a preliminary version of the theory. </pre> This method is described in Nielsen2012..."
- 12:0812:08, 6 March 2014 diff hist +6 SFS Estimation No edit summary
- 12:0812:08, 6 March 2014 diff hist +2 SFS Estimation No edit summary
- 12:0812:08, 6 March 2014 diff hist +64 SFS Estimation No edit summary
- 12:0612:06, 6 March 2014 diff hist +161 SFS Estimation →Options
- 12:0312:03, 6 March 2014 diff hist +67 SFS Estimation No edit summary
- 11:5311:53, 6 March 2014 diff hist −9 Thetas,Tajima,Neutrality tests →Example
- 11:5211:52, 6 March 2014 diff hist −9 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:5211:52, 6 March 2014 diff hist +4 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:5111:51, 6 March 2014 diff hist +4 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:5011:50, 6 March 2014 diff hist −4 Thetas,Tajima,Neutrality tests →Example
- 11:5011:50, 6 March 2014 diff hist +16 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:4611:46, 6 March 2014 diff hist +26 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:4411:44, 6 March 2014 diff hist +170 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:4011:40, 6 March 2014 diff hist +33 Thetas,Tajima,Neutrality tests →Sliding Window example
- 11:3811:38, 6 March 2014 diff hist +129 Thetas,Tajima,Neutrality tests →.thetas.gz is
- 11:3711:37, 6 March 2014 diff hist +67 Thetas,Tajima,Neutrality tests →Example
- 11:3611:36, 6 March 2014 diff hist −18 Thetas,Tajima,Neutrality tests →Sliding Window example
- 11:2711:27, 6 March 2014 diff hist +1 Thetas,Tajima,Neutrality tests →Example
- 11:2511:25, 6 March 2014 diff hist +72 Thetas,Tajima,Neutrality tests →Example
- 11:0911:09, 6 March 2014 diff hist +39 Thetas,Tajima,Neutrality tests →Example
5 March 2014
- 20:1520:15, 5 March 2014 diff hist +1 Filters →Extra
- 20:1420:14, 5 March 2014 diff hist +16 Plink →Example
- 20:1220:12, 5 March 2014 diff hist −11 Filters →Extra
- 20:1220:12, 5 March 2014 diff hist −2 Plink →Example
- 20:0920:09, 5 March 2014 diff hist 0 Plink No edit summary
- 20:0820:08, 5 March 2014 diff hist 0 Plink →Example
- 20:0120:01, 5 March 2014 diff hist −5 Plink No edit summary
- 20:0020:00, 5 March 2014 diff hist +38 MediaWiki:Sidebar No edit summary
- 19:3819:38, 5 March 2014 diff hist +29 Association →Example with imputation (using BEAGLE)
- 19:3619:36, 5 March 2014 diff hist +556 Association →Example with imputation (using BEAGLE)
- 19:3519:35, 5 March 2014 diff hist +279 Input →Genotype Probability Files
- 19:1819:18, 5 March 2014 diff hist −998 Bugs No edit summary
- 19:1019:10, 5 March 2014 diff hist +418 Association →Example
- 19:0619:06, 5 March 2014 diff hist −39 MediaWiki:Sidebar No edit summary
- 19:0519:05, 5 March 2014 diff hist +405 Beagle input →output
- 18:5918:59, 5 March 2014 diff hist −29 Beagle input →Example
- 18:5818:58, 5 March 2014 diff hist +139 Beagle input No edit summary
- 18:5418:54, 5 March 2014 diff hist −45 SNP calling No edit summary
26 February 2014
- 20:0420:04, 26 February 2014 diff hist +11 SNP calling No edit summary
- 18:4318:43, 26 February 2014 diff hist −43 Allele Frequencies →.mafs
- 18:4318:43, 26 February 2014 diff hist −1 Allele Frequencies →.mafs
- 18:4318:43, 26 February 2014 diff hist +8 Allele Frequencies →.mafs
- 18:4018:40, 26 February 2014 diff hist +105 Allele Frequencies →.mafs
- 18:3718:37, 26 February 2014 diff hist −606 Allele Frequencies →.mafs
- 18:3618:36, 26 February 2014 diff hist +44 Allele Frequencies →Allele Frequency estimation
- 18:3618:36, 26 February 2014 diff hist +974 N SYKmaf Created page with "==ML estimator with known minor== First infer the Major and Minor allele and then use BFGS (-doMaf 1) optimazation or the EM algorithm (..."
- 18:3518:35, 26 February 2014 diff hist +41 Allele Frequencies →Allele Frequency estimation
- 18:3518:35, 26 February 2014 diff hist −985 Allele Frequencies →Theory
- 18:3418:34, 26 February 2014 diff hist +64 Allele Frequencies No edit summary
- 18:3218:32, 26 February 2014 diff hist +11 User:Thorfinn No edit summary
- 18:3218:32, 26 February 2014 diff hist +867 User:Thorfinn →Anders changes to version 583
- 18:1318:13, 26 February 2014 diff hist +330 User:Thorfinn No edit summary
- 17:4717:47, 26 February 2014 diff hist +57 Allele Frequencies →Example
- 17:4617:46, 26 February 2014 diff hist −19 Allele Frequencies No edit summary
- 17:4517:45, 26 February 2014 diff hist −420 Allele Frequencies No edit summary
- 17:4417:44, 26 February 2014 diff hist +395 N PostFreq Created page with "==Estimator from genotype probabilities== If the genotype probabilities are known the frequencies can be estimated by summing up the posterior probabilities <math> p(G=g|D)</..." current
- 17:4417:44, 26 February 2014 diff hist −93 Allele Frequencies No edit summary
- 17:4117:41, 26 February 2014 diff hist +5 Allele Frequencies →Example
- 17:3917:39, 26 February 2014 diff hist +824 Allele Frequencies No edit summary
- 17:2517:25, 26 February 2014 diff hist +254 Error estimation No edit summary
- 17:2317:23, 26 February 2014 diff hist −75 Error estimation →Theory
- 17:2117:21, 26 February 2014 diff hist +15 Error estimation →Example
- 17:1917:19, 26 February 2014 diff hist +34 Error estimation →Options
- 17:1817:18, 26 February 2014 diff hist +15 Error estimation →Options
- 17:1617:16, 26 February 2014 diff hist +314 Error estimation →Error estimation using an outgroup and an error free individual
- 17:1517:15, 26 February 2014 diff hist +2,063 N ErrorPerfect Created page with "==Method 2== The method was use in Orlando2013 and is described in details in supplementary 4.4 The estimated rates can roughly be intrepreted as relative error rates. T..." current
- 17:1317:13, 26 February 2014 diff hist +28 Error estimation →Error estimation using an outgroup and an error free individual
- 17:1317:13, 26 February 2014 diff hist −2,065 Error estimation →Method 2
- 17:1217:12, 26 February 2014 diff hist −13 ErrorSykMethod No edit summary current
- 17:1217:12, 26 February 2014 diff hist +854 N ErrorSykMethod Created page with "==Method 1== The method is described in kim2011 and work by simultaneously estimating allele frequencies, genotype likelihoods and the error rates. The likelihood of t..."
- 17:1217:12, 26 February 2014 diff hist +69 Error estimation →Error estimation from polymorphic sites
- 17:1117:11, 26 February 2014 diff hist −856 Error estimation →Method 1
- 17:0817:08, 26 February 2014 diff hist +48 Error estimation →Output
- 17:0217:02, 26 February 2014 diff hist 0 Error estimation No edit summary
- 16:1716:17, 26 February 2014 diff hist +1 Error estimation No edit summary
- 16:1616:16, 26 February 2014 diff hist +11 Error estimation →Example
- 16:1216:12, 26 February 2014 diff hist +280 Error estimation No edit summary
- 16:0716:07, 26 February 2014 diff hist +16 Error estimation No edit summary
- 15:3315:33, 26 February 2014 diff hist 0 Major Minor No edit summary
- 15:2915:29, 26 February 2014 diff hist +503 Major Minor No edit summary
- 15:2315:23, 26 February 2014 diff hist +256 Major Minor →Details
- 15:1915:19, 26 February 2014 diff hist −29 Major Minor →From counts of data
- 15:1915:19, 26 February 2014 diff hist −1 Major Minor →From genotype likelihood data
- 15:1515:15, 26 February 2014 diff hist +1,283 N MajorMinor Method Created page with "==From Genotype Likelihoods== Assuming that the considered site is diallelic, we infer those two alleles using the genotype likelihoods. Let <math>\{M,m\}</math> denote the tw..." current