Variant Filtering and QC

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.

See Code

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)

See Code

Overlapping Genomic Regions of Interest

Overlapping Genomic Regions of Interest

This is a quick tutorial on finding genes near candidate SNPs using my favorite R package plyranges.

See Code