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Li2011
aalbrechtsen edited this page Sep 7, 2026
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Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, 27, 21:2987-93.
@Article{pmid21903627,
Author="Li, H. ",
Title="{{A} statistical framework for {S}{N}{P} calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data}",
Journal="Bioinformatics",
Year="2011",
Volume="27",
Number="21",
Pages="2987--2993",
Month="Nov"
}
doi: 10.1093/bioinformatics/btr509
</pre
Pages
Population genetics
Population structure
- Admixture
- Fst
- ABBABABA (D-stat)
- ABBABABA (multipop)
- Population branch statistics (pbs)
- PCA
- PCA (sampling approach)
- Linkage disequilibrium
Medical genetics
IBD/IBS
Summaries
SNPs and genotypes
- Genotypes likelihoods
- Major and Minor
- Allele frequencies
- Genotype calling
- Haploid calling
- SNP Calling
Output
Misc/util programs
Program structure
About ANGSD