precompile: g++ overlapping.cpp -o overlapping.o
Usage: pipeline.sh input.vcf 1000Genome.vcf
Step 1: convert VCF file to PLINK file
Step 2: filter variants with MAF>1%
Step 3: extract variants that were overlapped in both target dataset and 1000 Genome Projoect
Step 4: change the variant names to make it consistent across the two datasets
Step 5: combined the two datasets and perform PCA
Step 6: population stratification using KNN
Step 7: plot the first six principal components