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ANGSD
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NgsRelate
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PCAngsd
PCA, selection and inbreeding for NGS data
evalAdmix
evaluate admixture fit
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Example
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NGSadmix
Population Structure for NGS data
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Tutorial
asaMap
Ancestry-specific association mapping in admixed populations
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Citation
fastNGSadmix
admixture proportions and principal component analysis of a single NGS sample
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Input files
Running fastNGSadmix
PCA
Making a reference panel
Human reference panels
Citation
relateAdmix
Relatedness estimation for admixed individuals
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Example
LDadmix
Relate
Local IBD relatedness
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Manual
citation
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BAMSE
Bayesian Association of multiple SNPs
CATS
power for two stage GWAS
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various R scripts
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