admixture_pipeline

conda activate plink

plink --aec --out WEST --vcf WEST_filtered.recode.vcf

## --aec means allow exra chromosomes

cat WEST.fam | awk '{print $1}' > WEST.pop

cat WEST.fam | awk '{print $1,$2}' > WEST.list

#make indiv file by hand from

cat EAST3.pop | awk '{print ","$1}' > EAST3.indiv

sed -i 's/scaffold_//' WEST.bim

# filter with:

plink --bfile WEST --geno 0.1 --chr-set 67 no-xy --make-bed --out WEST2


#10/3/21
#thin raw SNPs with plink like in admixture manual

#####but first fix the var-IDs######

plink --bfile rawdata --geno 0.1 --chr-set 92 no-xy --set-missing-var-ids @:#[b37] --make-bed --out raw2

plink --aec --chr-set 92 no-xy --bfile raw2 --indep-pairwise 50 10 0.1

## try just –indep ##

plink --aec --chr-set 92 no-xy --bfile ../plinkfilter/raw2 --indep 50 5 2

plink --aec --chr-set 92 no-xy --bfile raw2 --extract plink.prune.in --make-bed --recode --out prunedData

##if you want to get a new thinned VCF

plink --bfile plinkfiltered --export vcf --out contigsplinkfiltered

#run ADMIXTURE

conda activate admixture

for k in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
  do
  admixture -j40 --cv WEST.bed $k | tee pop${k}.out
done