SNV calling from NGS data

SNV calling from NGS data is any of a range of methods for identifying the existence of single nucleotide variants (SNVs) from the results of next generation sequencing (NGS) experiments. These are computational techniques, and are in contrast to special experimental methods based on known population-wide single nucleotide polymorphisms (see SNP genotyping). Due to the increasing abundance of NGS data, these techniques are becoming increasingly popular for performing SNP genotyping, with a wide variety of algorithms designed for specific experimental designs and applications.[1] In addition to the usual application domain of SNP genotyping, these techniques have been successfully adapted to identify rare SNPs within a population,[2] as well as detecting somatic SNVs within an individual using multiple tissue samples.[3]

  1. ^ Nielsen, R., Paul, J. S., Albrechtsen, A., and Song, Y. S. (2011). "Genotype and SNP calling from next-generation sequencing data". Nature Reviews Genetics. 12 (6): 443–451. doi:10.1038/nrg2986. PMC 3593722. PMID 21587300.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ Bansal, V. (2010). "A statistical method for the detection of variants from next-generation resequencing of DNA pools". Bioinformatics. 26 (12): i318–i324. doi:10.1093/bioinformatics/btq214. PMC 2881398. PMID 20529923.
  3. ^ Roth, A., Ding, J., Morin, R., Crisan, A., Ha, G., Giuliany, R., Bashashati, A., Hirst, M., Turashvili, G., Oloumi, A., Marra, M. A., Aparicio, S., and Shah, S. P. (2012). "JointSNVMix: a probabilistic model for accurate detection of[somatic mutations in normal/tumour paired next-generation sequencing data". Bioinformatics. 28 (7): 907–913. doi:10.1093/bioinformatics/bts053. PMC 3315723. PMID 22285562.{{cite journal}}: CS1 maint: multiple names: authors list (link)