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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** depth|Depth | ** depth|Depth | ||
** base_quality|Base quality | ** base_quality|Base quality | ||
** fasta | Create Fasta file | |||
* | * SNPs and genotypes | ||
** Genotype_likelihoods_from_alignments|Genotypes likelihoods | ** Genotype_likelihoods_from_alignments|Genotypes likelihoods | ||
** Inferring_Major_and_Minor_alleles|Major and Minor | ** Inferring_Major_and_Minor_alleles|Major and Minor | ||
** Error estimation|Error estimation | ** Error estimation|Error estimation | ||
** Allele_Frequency_estimation|Allele frequencies | ** Allele_Frequency_estimation|Allele frequencies | ||
** | ** Genotype_calling|Genotype calling | ||
** SNP_calling|SNP Calling | |||
<!-- ** SNP_Calling|SNP Calling --> | <!-- ** SNP_Calling|SNP Calling --> | ||
<!-- ** Covariance_matrix_for_PCA|PCA --> | <!-- ** Covariance_matrix_for_PCA|PCA --> | ||
<!-- ** Heterozygosity|Heterozogosity --> | <!-- ** Heterozygosity|Heterozogosity --> | ||
<!-- ** HWE_and_Inbreeding_estimates|HWE and inbreeding --> | <!-- ** HWE_and_Inbreeding_estimates|HWE and inbreeding --> | ||
* | |||
* Population genetics | |||
**tajima|Thetas,Tajima,Neutrality test | **tajima|Thetas,Tajima,Neutrality test | ||
** HWE_and_Inbreeding_estimates|HWE and inbreeding | |||
** realSFS|SFS estimation | |||
* Population structure | * Population structure | ||
| Line 31: | Line 33: | ||
** Fst_PCA |Fst & PCA | ** Fst_PCA |Fst & PCA | ||
** Abbababa |ABBABABA (D-stat) | ** Abbababa |ABBABABA (D-stat) | ||
* Medical genetics | |||
** Association|Association | |||
* Output | * Output | ||
Revision as of 17:44, 2 December 2013
- Pages
- Main_Page#Overview|ANGSD overview
- Download_and_installation|Installation
- Quick_start|Quick start
- Input|Input data
- Summaries
- alleles_counts|Allele counts
- depth|Depth
- base_quality|Base quality
- fasta | Create Fasta file
- SNPs and genotypes
- Genotype_likelihoods_from_alignments|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
- Population genetics
- tajima|Thetas,Tajima,Neutrality test
- HWE_and_Inbreeding_estimates|HWE and inbreeding
- realSFS|SFS estimation
- Population structure
- NGSadmix | Admixture
- Fst_PCA |Fst & PCA
- Abbababa |ABBABABA (D-stat)
- Medical genetics
- Association|Association
- Output
- beagle_input|Beagle input files
- beagle_output | Beagle Output files
- Glf_files|Genotype likelihood files
- filters | Filter output
- Plink |Plink
- custom analysis
- 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