PCA

----------- In construction ------------

git clone [email protected]:jodyphelan/variant_calling.git
./variant_calling/extract_matrix.py [bcf|vcf file] > [output.txt]
R

#### Entering the R environment (quit with "control+d") ####

library(data.table)
library(amap)
dat<-as.data.frame(fread("output.txt"))
genos<-as.matrix(dat[,3:ncol(dat)])
dists<-Dist(t(genos),method="manhattan",nbproc=20)
pca<-cmdscale(dists)
plot(pca)

Pariwise distances histogram

lower_diag<-dists[lower.tri(dists,diag=F)]
hist(lower_diag)