Data Analysis - Initial O.lurida Fst Determination from GBS Data

2016
Genotype-by-sequencing at BGI
Olympia oyster reciprocal transplant
docker
dockerfile
FST
jupyter notebook
olympia oyster
Ostrea lurida
vcftools
Author

Sam White

Published

November 17, 2016

Finally running some analysis on the output from my PyRad analysison 20160727.

I’m following Katherine Silliman’s Jupyter notebook (2bRAD Subset Population Structure Analysis.ipynb) as a guide.

The initial analysis (which isn’t much) is in the Jupyter notebook below. The analysis will be continued on a later date.

Jupyter notebook: 20161117_docker_oly_vcf_analysis.ipynb

I’ve embedded the notebook below, but it’s much easier to view (there are many lengthy commands/filenames that wrap lines in the embedded version below) the actual file linked above.