![]() Some of these might in effect correspond to requiring the minor allele to be observed twice in an individual to be called. For this reason, more stringent criteria are typically used for calling SNPs and for calling heterozygote individuals. If multiple individuals are sampled, most SNPs will then in fact be errors. In 5X data, an error will then appear in at least 0.5% of all homozygotes, i.e. In most NGS, the error rate is at least 0.1% even after stringent filtering based on quality scores (e.g., ). Secondly, the high raw error rates often associated with NGS may cause a significant amount of homozygous genotypes to be wrongly inferred as heterozygous, if genotype calling is based on just absence/presence of an allele. First, in heterozygous individuals, both alleles may not have been sampled. In such data, genotype calling for each individual is associated with statistical uncertainty. While the price of NGS is declining, the demand for larger sample sizes is similarly increasing, suggesting that low or medium sequencing coverage may be the design of choice for many future studies in the years to come. Many NGS studies (e.g.,, , are based on medium to low coverage, i.e. However, the methods used in this paper may also be helpful for genotype and SNP calling in other studies based on multiple individuals, such as association mapping studies. In this paper, we will mostly be interested in population genetic applications. ![]() These technologies are used for de novo genome sequencing (e.g., ), in human disease genetics and diagnostics (e.g.,, ), in gene expression analyses (e.g., ), in population genetic studies (e.g., ), and in many other applications. The biological sciences have been transformed by the emergence of New-Generation Sequencing (NGS) technologies providing cheap and reliable large scale sequencing (e.g, ).
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |