Abstract:
:High-throughput DNA sequencing (HTS) is of increasing importance in the life sciences. One of its most prominent applications is the sequencing of whole genomes or targeted regions of the genome such as all exonic regions (i.e., the exome). Here, the objective is the identification of genetic variants such as single nucleotide polymorphisms (SNPs). The extraction of SNPs from the raw genetic sequences involves many processing steps and the application of a diverse set of tools. We review the essential building blocks for a pipeline that calls SNPs from raw HTS data. The pipeline includes quality control, mapping of short reads to the reference genome, visualization and post-processing of the alignment including base quality recalibration. The final steps of the pipeline include the SNP calling procedure along with filtering of SNP candidates. The steps of this pipeline are accompanied by an analysis of a publicly available whole-exome sequencing dataset. To this end, we employ several alignment programs and SNP calling routines for highlighting the fact that the choice of the tools significantly affects the final results.
journal_name
Hum Genetjournal_title
Human geneticsauthors
Altmann A,Weber P,Bader D,Preuss M,Binder EB,Müller-Myhsok Bdoi
10.1007/s00439-012-1213-zsubject
Has Abstractpub_date
2012-10-01 00:00:00pages
1541-54issue
10eissn
0340-6717issn
1432-1203journal_volume
131pub_type
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