JOURNAL OF ANIMAL SCIENCE AND VETERINARY MEDICINE
Integrity Research Journals
ISSN: 2536-7099
Model: Open Access/Peer Reviewed
DOI: 10.31248/JASVM
Start Year: 2016
Email: jasvm@integrityresjournals.org
Variant Calling pipeline for Next Generation Sequence Data – A review
https://doi.org/10.31248/JASVM2018.092 | Article Number: 49FBD3E01 | Vol.3 (4) - August 2018
Received Date: 20 February 2018 | Accepted Date: 30 April 2018 | Published Date: 30 August 2018
Author: Ngeno K.
Keywords: SNP., Next-generation sequencing, Annotation
Next generation sequencing (NGS) is of great significance for genetic improvement. Some of the most common application of NGS is the identification of the genomic variants, genes and sequence mutations. Mining of genomic variants such as single nucleotide polymorphisms (SNPs) from raw sequences involves several steps and use of numerous bioinformatics tools in a systematic manner. This paper reviews the components of a pipeline that calls SNPs from NGS data. The SNP calling pipeline includes base calling, quality checks, reads trimming, alignment of the quality reads to the reference genome, quality score recalibration, visualization and SNP identification. The final step of the pipeline is making biological sense out of the SNPs data, which involves filtering and annotation of the candidates SNPs.
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