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RAW or VCF annotation is the process of adding additional information to a VCF (variant call format) file, (RAW files are converted to VCF before annotating them) which is a standard file format used to store DNA sequence variations, such as single nucleotide polymorphisms (SNPs) and small insertions and deletions. VCF annotation can involve adding information about the functional consequences of the variations, such as whether they are likely to have an impact on the protein encoded by the gene, or whether they have been associated with a particular disease or trait.
What is Clinvar?
CLINVAR is a database of genetic variations that have been associated with clinical phenotypes (observable characteristics or traits). It is maintained by the National Center for Biotechnology Information (NCBI), which is part of the National Institutes of Health (NIH).
CLINVAR is a publicly available resource that is used by researchers, clinicians, and other healthcare professionals to help understand the relationship between genetic variations and various diseases and conditions. It contains information about genetic variants that have been reported in the scientific literature, as well as those submitted directly by researchers.
The database is updated regularly, and includes information about the type of variant, the gene in which it occurs, the clinical significance of the variant (e.g., pathogenic, benign, or uncertain), and any relevant citations. CLINVAR is a valuable resource for understanding the role of genetics in human health, and is used by researchers and healthcare professionals around the world.
How is the VCF annotated using CLINVAR?
One way to perform VCF annotation is by using the CLINVAR database, which is a public database of genetic variations with known clinical significance. CLINVAR contains information about variations that have been associated with inherited conditions, as well as variations that are of uncertain clinical significance. By using CLINVAR, it is possible to identify variations in a VCF file that have been previously reported as having a potential clinical impact and to add this information to the VCF file for further analysis.
VCF annotation using CLINVAR can be useful for a variety of purposes, such as identifying genetic risk factors for inherited conditions, evaluating the potential impact of genetic variations on drug response, or aiding in the diagnosis of rare genetic disorders. It can also be used to help prioritize variations for further study and to aid in the interpretation of genetic test results.
