User contributions for Albrecht

18 June 2012

• 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
• 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..."