In rare disease genetic testing whole genome sequencing is a comprehensive technology to address the limitations of gene panels and exome analysis. The latter use selective capturing of target regions. Only WGS is able to provide sufficient coverage of the coding region of the genome especially for GC-rich regions.
In this context it becomes evident that in order to find rare but valuable variants related to genetic disorders, the use of the full genome sequence as starting input is clinically essential.
The Foundation of People with Rare Diseases is constantly on the outlook to improve the performance of their whole genome analysis process. Dealing with large-scale whole genome sequencing requires read mapping and variant calling solutions which deliver fast turn around times, manageable output file size and high variant calling accuracy. Their most recent study in which 4 analysis pipelines were compared has been published on line in PNAS at http://www.pnas.org/content/early/2017/09/14/1713830114.short?rss=1
The four pipelines include BWA/ GATK, GENALICE MAP, PEMapper/PECaller and Isaac. The experiment assessed sensitivy/recall, precision, computation time and disk footprint. It is concluded that in the field of accurate whole-genome data analysis GENALICE MAP challenges BWA/GATK more than PEMapper/PECaller and Isaac.