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.
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* Output | * Output | ||
** beagle_input|Beagle input files | ** beagle_input|Beagle input files | ||
** Glf_files|Genotype likelihood files | ** Glf_files|Genotype likelihood files | ||
** Plink |Plink | ** Plink |Plink | ||
Revision as of 18:06, 5 March 2014
- Pages
- Main_Page#Overview|ANGSD overview
- Download_and_installation|Installation
- Quick_Start|Quick Start/Testdata
- Input|Input data
- filters | Filters
- Population genetics
- tajima|Thetas,Tajima,Neutrality test
- HWE_and_Inbreeding_estimates|HWE and inbreeding
- SFS Estimation|SFS Estimation
- Population structure
- NGSadmix | Admixture
- Fst_PCA |Fst & PCA
- Abbababa |ABBABABA (D-stat)
- Medical genetics
- Association|Association
- Summaries
- alleles_counts|Allele counts
- depth|Depth
- base_quality|Base quality
- fasta | Create Fasta file
- SNPs and genotypes
- Genotype_likelihoods|Genotypes likelihoods
- Inferring_Major_and_Minor_alleles|Major and Minor
- Error estimation|Error estimation
- Allele_Frequency_estimation|Allele frequencies
- Genotype_calling|Genotype calling
- SNP_calling|SNP Calling
- Output
- beagle_input|Beagle input files
- Glf_files|Genotype likelihood files
- Plink |Plink
- Misc/util programs
- emOptim2 | emOptim2
- msToGlf | msToGlf
- thetaStat | thetaStat
- supersim | supersim
- Program structure
- angsd structure |Introduction
- angsd_class | overview of class
- custom_start | getting started
- data_access | accessing core data
- custom_data | custom data containers
- print | printing results
- About ANGSD
- change_log|Version log
- citing_angsd|Citing angsd
- authors|Authors
- Bugs | Bugs
- navigation
- mainpage|mainpage-description
- portal-url|portal
- currentevents-url|currentevents
- recentchanges-url|recentchanges
- randompage-url|randompage
- helppage|help
- SEARCH
- TOOLBOX
- LANGUAGES