Apple Variant Calling Notes
The purpose of this project is to call and utalizie the software GATK from the broad institue to call variants on a set of highly diverse apple read sets. This is in an effort to learn more about the apple genome and get a sense of the genomic diversity of the apple genome.
This github is simple a collection of all the scripts I ran in order, and what the purpose of each script was. Something useful that you may want to note is that I utalizied bootstrapping to manufacture a golden snp set from a non model organism. We did this following the GATK guidlines from the broad. NOTE: this method is still unverrified by the broad... but everyone does it.
All scripts are written in bash, and hopefully one day this pipeline will be converted to a modern pipeline language like nextflow or snakemake, but that's for the future.
Name Of Script: