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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