Variant Filtering and QC
This is a pipeline to generate a filtered SNP .vcf file from raw .fastq files. The approach is designed for hundreds of whole-genome low coverage sequences.
Using the FARM Computer Cluster
A tutorial on how to submit jobs on the UC Davis FARM cluster. Developed for ECL243 (Ecological Genomics graduate level course)
Overlapping Genomic Regions of Interest
This is a quick tutorial on finding genes near candidate SNPs using my favorite R package plyranges.