High-Throughput Sequencing (HTS) has made it possible to discover genetic variants and carry out genome-wide genotyping and haplotyping in many samples in a short space of time. The deluge of data that this technology has released has created some unique opportunities for bioinformaticians and computer scientists, and some really innovative new data storage and data analysis pipelines have been created. The fundamental pipeline in variant calling starts with the quality control of HTS reads and the alignment of those reads to a reference genome. These steps invariably take place before analysis in R and typically result in a BAM file of read alignments or a VCF file of variant positions (see the Appendix of this book for a brief discussion of these file formats) that we'll want to process in our R code.
As variant calling and analysis...
