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
- 15:2615:26, 18 June 2012 diff hist −21 ANGSD →Heterozygosity
- 15:2615:26, 18 June 2012 diff hist −1,603 ANGSD →Full example for simulating nextgen data and estimating SFS (somewhat deprecated should use sfstools now)
- 15:2515:25, 18 June 2012 diff hist +1,603 SFS Estimation No edit summary
- 15:2515:25, 18 June 2012 diff hist −686 ANGSD →Download and Installation
- 15:2415:24, 18 June 2012 diff hist +380 Installation No edit summary
- 15:2115:21, 18 June 2012 diff hist −2,753 ANGSD →Association
- 15:2115:21, 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..."
- 15:2115:21, 18 June 2012 diff hist −97 MediaWiki:Sidebar No edit summary
- 15:2015:20, 18 June 2012 diff hist +97 MediaWiki:Sidebar No edit summary
- 15:1915:19, 18 June 2012 diff hist +29 N Covariance matrix for PCA Created page with "==Covariance matrix for PCA==" current
- 15:1915:19, 18 June 2012 diff hist −31 ANGSD →Covariance matrix for PCA
- 15:1815:18, 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..."
- 15:1815:18, 18 June 2012 diff hist −747 ANGSD →SNP Calling
- 15:1815:18, 18 June 2012 diff hist +27 MediaWiki:Sidebar No edit summary
- 15:1815:18, 18 June 2012 diff hist +125 N Genotype Likelihoods Created page with "==Genotype likelihoods from alignments== ===Kim et al.=== Citation Citation ===Samtools=== ===GATK==="
- 15:1715:17, 18 June 2012 diff hist −127 ANGSD →Genotype likelihoods from alignments
- 15:1715:17, 18 June 2012 diff hist −780 ANGSD →Genotype calling
- 15:1715:17, 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..."
- 15:1715:17, 18 June 2012 diff hist +17 MediaWiki:Sidebar No edit summary
- 15:1615:16, 18 June 2012 diff hist +20 MediaWiki:Sidebar No edit summary
- 15:1515:15, 18 June 2012 diff hist +2 MediaWiki:Sidebar No edit summary
- 15:1515:15, 18 June 2012 diff hist −238 ANGSD →dumping counts
- 15:1515:15, 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,..."
- 15:1415:14, 18 June 2012 diff hist +44 MediaWiki:Sidebar No edit summary
- 15:1415:14, 18 June 2012 diff hist −86 ANGSD →Error estimation
- 15:1415:14, 18 June 2012 diff hist +84 N Error estimation Created page with "==Error estimation== ===Kim et al.=== Citation ===Using an outgroup==="
- 15:1315:13, 18 June 2012 diff hist −336 ANGSD →realSFS
- 15:1315:13, 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 ..."
- 14:5514:55, 18 June 2012 diff hist +2 Allele Frequencies →Example
- 14:5514:55, 18 June 2012 diff hist +174 Allele Frequencies →Estimator from genotype probabilities
- 14:5314:53, 18 June 2012 diff hist +397 Allele Frequencies →Allele frequencies from genotype likelihoods
- 13:4413:44, 18 June 2012 diff hist +91 Allele Frequencies →Estimator from sequencing data
- 12:2712:27, 18 June 2012 diff hist +1 Allele Frequencies →ML estimator with known minor
- 12:2712:27, 18 June 2012 diff hist +2 Allele Frequencies →Allele Frequency estimation
- 12:2612:26, 18 June 2012 diff hist +305 Allele Frequencies No edit summary
- 11:1511:15, 18 June 2012 diff hist +1,576 Allele Frequencies No edit summary
15 June 2012
- 10:1410:14, 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..."
- 10:1410:14, 15 June 2012 diff hist +4 Allele Frequencies No edit summary
- 10:1310:13, 15 June 2012 diff hist +229 Allele Frequencies No edit summary
14 June 2012
- 21:0221:02, 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..."
- 20:5920:59, 14 June 2012 diff hist −242 ANGSD →Allele Frequency estimation
- 20:5920:59, 14 June 2012 diff hist −460 ANGSD →Inferring Major and Minor alleles
- 20:4120:41, 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
- 20:4120:41, 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..."
- 20:4020:40, 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
- 20:3920:39, 14 June 2012 diff hist +1,015 Major Minor No edit summary
- 19:2319:23, 14 June 2012 diff hist −3 Input →optional arguments
- 19:2319:23, 14 June 2012 diff hist +179 Input →optional arguments
- 19:2119:21, 14 June 2012 diff hist +181 Input →obtional arguments
- 18:4518:45, 14 June 2012 diff hist +569 Input →bam files