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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* Pages
* Pages
** popgen.dk/wiki/index.php/Main_Page#Download|dirty
** Main_Page#Overview|ANGSD overview
** popgen.dk/wiki/index.php/Main_Page#Installation|Installation
** Download_and_installation|Installation
** popgen.dk/wiki/index.php/Main_Page#Overview|Overview
** Quick_Start|Quick Start/Testdata
** popgen.dk/wiki/index.php/Main_Page#All_options|options
** Input|Input data
** popgen.dk/wiki/index.php/Main_Page#Input_data|input data
** filters | Filters
** popgen.dk/wiki/index.php/Main_Page#Output_data|output data
** snpFilters | snpFilters
* Methods


** popgen.dk/wiki/index.php/Main_Page#realSFS|realSFS
* Population genetics
** popgen.dk/wiki/index.php/Main_Page#Genotype_likelihoods_from_alignments|Genotypes likelihoods
** SFS Estimation|SFS Estimation
** popgen.dk/wiki/index.php/Main_Page#Inferring_Major_and_Minor_alleles|Major and Minor
**tajima|Thetas,Tajima,Neutrality test
** popgen.dk/wiki/index.php/Main_Page#Error_estimation|Error estimation
** 2d SFS Estimation |(Multi) SFS Estimation
** popgen.dk/wiki/index.php/Main_Page#Allele_Frequency_estimation|Allele frequencies
** Direct Ancestry | Direct Ancestry
** popgen.dk/wiki/index.php/Main_Page#SNP_Calling|SNP Calling
*  Population structure
** popgen.dk/wiki/index.php/Main_Page#Covariance_matrix_for_PCA|PCA
** NGSadmix | Admixture
** popgen.dk/wiki/index.php/Main_Page#Association|Association
** Fst |Fst
** popgen.dk/wiki/index.php/Main_Page#Heterozygosity|Heterozogosity
** Abbababa |ABBABABA (D-stat)
** popgen.dk/wiki/index.php/Main_Page#HWE_and_Inbreeding_estimates|HWE and inbreeding
** Abbababa2 |ABBABABA (multipop)
** Pbs | Population branch statistics (pbs)
** PCA | PCA
** PCA_MDS | PCA (sampling approach)
** LD | Linkage disequilibrium
 
 
* Medical genetics
** Association|Association
 
* IBD/IBS
** Relatedness | Relatedness
** HWE_and_Inbreeding_estimates|HWE and inbreeding with ngsF
** HWE_test | HWE test
** Genotype_Distribution | Genotype distribution
** Heterozygosity | Heterozygosity
 
* Summaries
** Contamination|Contamination
** Error estimation|Error estimation
** alleles_counts|Allele counts
** depth|Depth
** base_quality|Base quality
** fasta | Create Fasta file
** Mismatch | Mismatch
 
 
* SNPs and genotypes
** Genotype_likelihoods|Genotypes likelihoods
** Inferring_Major_and_Minor_alleles|Major and Minor
** Allele_Frequency_estimation|Allele frequencies
** Genotype_calling|Genotype calling
** Haploid_calling|Haploid calling
** SNP_calling|SNP Calling
<!-- ** SNP_Calling|SNP Calling -->
<!-- ** Covariance_matrix_for_PCA|PCA -->
<!-- ** Heterozygosity|Heterozogosity -->
<!-- ** HWE_and_Inbreeding_estimates|HWE and inbreeding -->
 
* Output
** beagle_input|Beagle inputation
** Genotype_likelihoods#Output_genotype_likelihoods|Genotype likelihood files
** Plink |Plink
 
*Misc/util programs
** realSFS | realSFS
** 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




Latest revision as of 09:54, 17 July 2019

  • Pages
    • Main_Page#Overview|ANGSD overview
    • Download_and_installation|Installation
    • Quick_Start|Quick Start/Testdata
    • Input|Input data
    • filters | Filters
    • snpFilters | snpFilters
  • Population genetics
    • SFS Estimation|SFS Estimation
    • tajima|Thetas,Tajima,Neutrality test
    • 2d SFS Estimation |(Multi) SFS Estimation
    • Direct Ancestry | Direct Ancestry
  • Population structure
    • NGSadmix | Admixture
    • Fst |Fst
    • Abbababa |ABBABABA (D-stat)
    • Abbababa2 |ABBABABA (multipop)
    • Pbs | Population branch statistics (pbs)
    • PCA | PCA
    • PCA_MDS | PCA (sampling approach)
    • LD | Linkage disequilibrium


  • Medical genetics
    • Association|Association
  • IBD/IBS
    • Relatedness | Relatedness
    • HWE_and_Inbreeding_estimates|HWE and inbreeding with ngsF
    • HWE_test | HWE test
    • Genotype_Distribution | Genotype distribution
    • Heterozygosity | Heterozygosity
  • Summaries
    • Contamination|Contamination
    • Error estimation|Error estimation
    • alleles_counts|Allele counts
    • depth|Depth
    • base_quality|Base quality
    • fasta | Create Fasta file
    • Mismatch | Mismatch


  • SNPs and genotypes
    • Genotype_likelihoods|Genotypes likelihoods
    • Inferring_Major_and_Minor_alleles|Major and Minor
    • Allele_Frequency_estimation|Allele frequencies
    • Genotype_calling|Genotype calling
    • Haploid_calling|Haploid calling
    • SNP_calling|SNP Calling
  • Output
    • beagle_input|Beagle inputation
    • Genotype_likelihoods#Output_genotype_likelihoods|Genotype likelihood files
    • Plink |Plink
  • Misc/util programs
    • realSFS | realSFS
    • 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
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