2.4 Summary of genomics technologies

The different technologies described above have different pros and cons. Generally:

• SNP arrays are cheapest and best for assaying common SNPs in a large number of samples

• NGS gives a more comprehensive view of genetic variation, including rare variants and many more complex variants such as indels and some types of structural variants

• Long-reads can sequence the majority of human genome, include repeats and complex regions. However, it has higher error rates (this is changing rapidly), is more expensive, and is not yet as widely available.

While we will always need to be aware of where the data we are using came from, for most of our analyses we will focus on downstream applications of the resulting SNP genotypes, rather than of analysis of raw genotyping or sequencing data ourselves.