Biological Data Science: Saving Lives with Software - Hadoop: The Definitive Guide - page 797

▪ A single-nucleic polymorphism (SNP), pronounced “snip,” is a single-character
change in the source code (e.g., from ACT G ACTG to ACT T ACTG ).
▪ An indel is short for insert-delete and represents an insertion or deletion from the
reference genome. For example, if the reference has CCTGACTG and your sample
has four characters inserted — say, CCTG CCTA ACTG — then it is an indel.
▪ Only 0.5% of the source gets translated into the proteins that sustain your life.
That portion of the source is called your exome . A human exome requires a few
gigabytes to store in compressed binary files.
▪ The other 99.5% of the source is commented out and serves as word padding ( in-
trons ); it is used to regulate when genes are turned on, repeat, and so on. [ 157 ] A
whole genome requires a few hundred gigabytes to store in compressed binary
files.
▪ Every cell of your body has the same source, [ 158 ] but it can be selectively com-
mented out by epigenetic factors like DNA methylation and histone modification ,
not unlike an #ifdef statement for each cell type (e.g., #ifdef RETINA or
#ifdef LIVER ). These factors are responsible for making cells in your retina
operate differently than cells in your liver.
▪ The process of variant calling is similar to running diff between two different
DNA sources.
These analogies aren't meant to be taken too literally, but hopefully they helped familiar-
ize you with some genomics terminology.