Part 1:  Population structure

  1. Bring in SNP data in gd_snp format from the Galaxy library
  2. Find the coverage distribution of the sequence reads
  3. Draw a phylogenetic tree using all the SNPs
  4. Convert the gd_snp file and filter SNPs
  5. Run an principal component analysis on the converted SNPs
  6. Group the individuals using information from the tree and PCA
  7. Prepare an input dataset without the outlier
  8. Run the PCA with labels and no outlier
  9. Graph the ancestry of the individuals
Note: This tutorial assumes some basic Galaxy skills are already known. If this is your first time using Galaxy, doing an earlier example first will help.