Variant Call Analysis

Identifying single nucleotide polymorphisms and small insertions and deletions from next-generation sequencing data, then annotating and filtering them.

Read the rendered analysis: https://beatrizmclm.github.io/3.Variant_Call_Analysis/

What it covers

Part 1. Calling variants

• Indexing a BAM file and calling variants into VCF against a chromosome 7 reference
• Annotation through Ensembl VEP and inspection in the NCBI Genome Browser

Part 2. Annotating and filtering in R

• Reading VCF and reference genome with the VariantAnnotation package
• Examining header information and genomic positions
• Filtering variants on quality and annotation

Contents

File
BGA Practical 3 - Variant Call Analysis.Rmd	Source, with commentary
index.html	Knitted output, served at the link above

R, Bioconductor, VariantAnnotation, Ensembl VEP. MSc Bioinformatics coursework, University of West London.