1_clean_data.md

./scripts/1_clean_data.sh

All commands to be run in the terminal

Remove loci not placed on a chromosome.

Create a new data set (in ./work/) only including loci that are placed on one of the 26 chromsomes in pink salmon. Call it "pink_salmon.clean". The --make-bed command tells Plink to create pink_salmon.bed (binary file with genotype data), pink_salmon.bim (text with locus information ) and ./pink_salmon.fam (text file with sample information) files.

When using Plink to analyze data from non-human species, it is important to tell Plink to not interpret chromosome "23" as the X chromosome and chromosome "24" as the Y chromsome (this is true for humans, and is the default configuration in Plink).

plink --bfile ./data/pink_salmon --autosome-num 26 --not-chr 0 --make-bed --out ./work/pink_salmon.clean

Create a separate set of genotype data files for each population.

For each of the six populations of pink salmon, select just the individuals in the population and then filter for HWE, genotyping rate per locus, and minor allele frequency.

plink --bfile ./work/pink_salmon.clean --family --keep-cluster-names Koppen_ODD --hwe .001 --geno 0.02 --maf 0.05 --make-bed --out ./work/Koppen_ODD

plink --bfile ./work/pink_salmon.clean --family --keep-cluster-names Koppen_EVEN --hwe .001 --geno 0.02 --maf 0.05 --make-bed --out ./work/Koppen_EVEN

plink --bfile ./work/pink_salmon.clean --family --keep-cluster-names Nome_ODD --hwe .001 --geno 0.02 --maf 0.05 --make-bed --out ./work/Nome_ODD

plink --bfile ./work/pink_salmon.clean --family --keep-cluster-names Nome_EVEN --hwe .001 --geno 0.02 --maf 0.05 --make-bed --out ./work/Nome_EVEN

plink --bfile ./work/pink_salmon.clean --family --keep-cluster-names Puget_ODD --hwe .001 --geno 0.02 --maf 0.05 --make-bed --out ./work/Puget_ODD

plink --bfile ./work/pink_salmon.clean --family --keep-cluster-names Puget_EVEN --hwe .001 --geno 0.02 --maf 0.05 --make-bed --out ./work/Puget_EVEN