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Lizhong Wang edited this page Apr 21, 2017 · 8 revisions

PCA

Short for Principal Component Analysis , calculate with smartpca in EIGENSOFT.

Run like this: smartpca -p smartpca.par >smartpca.par.log.

Prepare a parameter file smartpca.par like this:

# input
genotypename: input.ped
snpname:      input.map
indivname:    input.pedind

# output
evecoutname:  PCAout.evec
evaloutname:  PCAout.eigenvalues

# optional parameters
numoutevec:          4
numoutlieriter:      0
altnormstyle:        NO
numoutlierevec:      10
outliersigmathresh:  6
qtmode:              0

# Multi-threading parameters
numthreads:          10

# output EIGENSTRAT files
outputformat:      EIGENSTRAT
genotypeoutname:   input.EIGENSTRAT.geno
snpoutname:        input.EIGENSTRAT.snp
indivoutname:      input.EIGENSTRAT.ind

More details in README of smartpca.

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