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• 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 (without SNP calling)
  • PCA_MDS | PCA/MDS (with SNP calling)
• 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
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