Chapter 28 Bioinformatic analysis on variant data

Standard analyses like computing Fst and linkage disequilibrium, etc., from data, typically in a VCF file.

Basically, we want to get comfortable with plink 2.0, bedtools, vcftools, etc.

The key in all of this is to motivate every single thing we do here in terms of an application in conservation genomics. That is going to be key.

This Part IV will be about standard bioinformatic tools for doing things with big variant data.

  • Filtering
  • Imputation
  • LD, HWD, FST
  • Etc.

I will probably have a chapter on unix tools.

Maybe another on R/Bioconductor tools.

Gotta have a chapter about “Look at your data!” and Whoa! and diagnostics using radiator.