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Table 1 Advantages and Disadvantages for the use of NGS data in genetic background characterization

From: Streamlined computational pipeline for genetic background characterization of genetically engineered mice based on next generation sequencing data

 

Genotype Variants Pipeline

SNP genotyping

Implementation

NGS data: WGS/WES/RNA-seq

Only microarrays

Computational Resources

High for WES/WGS

Low

Rare Variant Detection

Yes

Difficult

Novel variant discovery

Yes

No

QTL detection

Yes, Using RNA-Seq (eQTLs)

Yes, using genetic linkage studies.

Sensibility

Increasing power with more depth

Fixed

Visualisation

Genome wide-plots in R (free)

Programatically or included in commercial programs

  1. We reviewed the advantages and disadvantages in genetic monitoring using NGS data (through our pipeline) versus SNP-dense microarrays. We considered implementation, computational resources, rare variant detection, novel variant discovery, QTL detection, sensibility and visualization in each method