Description of variant calling
Genetic variation is a type of variation that can be inherited to offspring caused by changes in the genetic material of an organism. It is this variation that causes organisms to exhibit genetic diversity at different levels. Genetic diversity is the material basis for the survival and development of living species. There are many types of genetic variation, from microscopically visible chromosome inversion to single nucleotide mutations. With the development of genomics, genetic variation information has become more comprehensive and has included SNP, InDel, SV, CNV, and transposon mutations.
Variant calling refers to the use of high-throughput sequencing technology to sequence and analyze the differences in the entire genome of an individual or population of a species, to obtain a large amount of genetic variation information, such as Single Nucleotide Polymorphism (SNP) , Insertion and deletion sites (InDel) and structural variation sites (SV), copy number variation (CNV) and other information. Variant calling can provide the most basic and comprehensive data foundation for subsequent functional gene fine mapping and quickly, accurately and efficiently analyze the differences between genomes, analyze each base of the whole genome, and obtain the most extensive molecular markers.
Advantages and features of variant calling
- Abundance: In-depth analysis of all aspects of genetic variation, including SNP, InDel, SV, SNV.
- Flexibility: with or without reference is suitable
- Accuracy: different sequencing methods can be applied based on different material
Variant calling workflow
Sequencing technology pipeline
- Based on whole genome assembly
- Based on whole genome resequencing
- Based on reduced-representation genome sequencing
- Jansen S, Aigner B, Pausch H, et al. Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage[J]. BMC Genomics, 2013, 14(1): 1.
- Zheng L Y, Guo X S, He B, et al. Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)[J]. Genome Biology, 2011, 12(11):287-302.