VariantAnnotation Example

Script to annotate genetic variants from VCF file.

Description

This script first takes a .vcf file and converts it a GRanges data object. It then creates a separate data frame of annotations including the depth of sequence coverage, variant type, alternate allele frequency, and a few others. Lastly, it saves this annotation data frame as a .csv file in the working directory.

Locations of answers to challenge questions in output file

var.type and var.effect columns
depth column
var.num column
percent.var and percent.ref columns
not completed
perc.ref.for

Link to GitHub repo

Getting Started

Dependencies

Make sure you have the following packages installed from CRAN or Bioconductor.

BiocManager::install("VariantAnnotation")
install.packages("here")
BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGen")

Installing

No installation necessary

Executing program

Create a directory that contains the script and the VCF data file.
Open R from that directory.
Simply run script from top to bottom.

Help

Contact the Author.

Authors

ex. Abby Spangler
ex. LinkedIn

Acknowledgments

Inspiration, most helpful packages, etc.

VariantAnnotation

Thank you for interviewing me, Tempus!

abspangler13/VariantAnnotation