MediaWiki:Sidebar: Difference between revisions

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

@@ Line 6: / Line 6: @@
 ** filters | Filters
 ** snpFilters | snpFilters
 * Population genetics
 ** SFS Estimation|SFS Estimation
 **tajima|Thetas,Tajima,Neutrality test
-** HWE_and_Inbreeding_estimates|HWE and inbreeding
 ** 2d SFS Estimation |(Multi) SFS Estimation
+** Direct Ancestry | Direct Ancestry
 *  Population structure
 ** NGSadmix | Admixture
@@ Line 16: / Line 17: @@
 ** Abbababa |ABBABABA (D-stat)
 ** Abbababa2 |ABBABABA (multipop)
+** Pbs | Population branch statistics (pbs)
+** PCA | PCA
+** PCA_MDS | PCA (sampling approach)
+** LD | Linkage disequilibrium
-** NgsRelate | Relatedness
-** Pbs | Population branch statistics (pbs)
-** PCA | PCA
 * 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
@@ Line 30: / Line 41: @@
 ** fasta | Create Fasta file
 ** Mismatch | Mismatch
 * 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
@@ Line 53: / Line 65: @@
 ** thetaStat | thetaStat
 ** supersim | supersim
 * Program structure
 ** angsd structure |Introduction

MediaWiki:Sidebar: Difference between revisions

Latest revision as of 09:54, 17 July 2019

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