This course offers an overview of current massive parallel sequencing data paying special attention to those produced by the Illumina short-read sequencing technology from genomic DNA and its main applications to Genomics Research. Additionally, provides a basic training in bioinformatics techniques for handling, managing and analysing sequencing data. We will follow the main workflows of the Broad Institute for calling Single Nucleotide Variants (SNVs) or Indels with GATK. Additionally, we will do several exercises for handling, filtering and extracting information from VCFs and GVCFs. Finally, these data will allow the estimation of classical population genetics statistics, keeping in mind that they could also be computed at genomic scale.