Using Integrative Genomic Viewer (IGV) to Inspect for Genomic Heterozygosity
Guide to using this helpful genetics tool
There are many valuable tools for a research scientist in genetics. One such tool is the Integrative Genomics Viewer. This program has several functions useful for someone looking at sequencing data. I will be going over a focused function for one seeking to grab select data quickly.
Homozygous or Heterozygous?
Heterozygosity has implications on physical traits and the strength of a harmful effect. Inspecting for this is fortunately relatively easy. After loading a genome file, zoom into your desired locus by entering the locus into the bar at the top of the screen:
Next, zoom out using the zoom bar at the top right (seen in the above image) to where you can see the different reads:
Non-reference SNPs are indicated by non-grey colorings, such as the blue lines and green lines. Homozygous would be characterized by having the same color at a given site, such as green for all reads on the left-most SNP. Heterozygous could be indicated by mixed colors, like one read…
