Hi,
I am a beginner in PopGen, and I am using smartPCA for my research. So far, I encountered several questions:
1. My genotype data is seperated by chromosome in each file. Currently I am testing my scripts with chr22 only. Do I need to pool them toghther in to one file to do smartPCA?
2. It seems that smartPCA will raise an error if the phenotype column in input file is empty (for instance, 0 for all individuals). However, I think phenotype data is not needed for PCA. Do I need the actual phenotype data to run the program?
Thanks!
Well, I have solved this problem by reading papers.
1. Doing genome-wide PCA requires merging the files together. The good news is that SNPs used in PCA should be pruned or "thined". So typically only about 20,000 SNPs are used, making the merged file small.
2. PLINK file is recommended to be converted to EIGENSTRAT format using convertf. The convertf tool accept PLINK format as input, but smartpca does not.