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 | ||
** Main_Page#Overview| | ** Main_Page#Overview|ANGSD overview | ||
** Download_and_installation|Installation | ** Download_and_installation|Installation | ||
** Input| | ** 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 | * Summaries | ||
** alleles_counts| | ** 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 | ** Inferring_Major_and_Minor_alleles|Major and Minor | ||
** Allele_Frequency_estimation|Allele frequencies | ** Allele_Frequency_estimation|Allele frequencies | ||
** | ** Genotype_calling|Genotype calling | ||
** | ** Haploid_calling|Haploid calling | ||
** | ** SNP_calling|SNP Calling | ||
** Heterozygosity|Heterozogosity | <!-- ** SNP_Calling|SNP Calling --> | ||
** HWE_and_Inbreeding_estimates|HWE and inbreeding | <!-- ** Covariance_matrix_for_PCA|PCA --> | ||
** Genotype | <!-- ** 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 | |||
* navigation | * navigation | ||
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