How to understand gnomAD database
How to understand the gnomAD database, many novices are not very clear about this, in order to help you solve this problem, the following editor will explain for you in detail, people with this need can come to learn, I hope you can gain something.
GnomAD is an academic consortium that collects and collates a variety of large-scale exon and whole genome sequencing data and is available free of charge around the world. In its first version, only exon sequencing data was included, called Exome Aggregation Consortium (ExAc).
The latest version is 2.0.2, updated on October 3, 2017. The variation information in the database is based on hg19, and the database also contains data from different populations.
On the website, genes or transcripts can be easily searched. The interested gene or transcript can be output in the input box in the upper left corner, and the mutation sites related to the gene or transcript will be given in the search results. Examples are as follows
Http://gnomad.broadinstitute.org/gene/ENSG00000160349
1. Basic information of genes
Information such as gene name, number of mutation sites contained, and links to other databases
two。 Coverage information
Blue represents exon sequencing data, and green represents genome-wide sequencing data.
3. Details of the variation site
The VEP software is used to annotate the variation sites.
The download address is also provided on the official website at the following URL
Http://gnomad.broadinstitute.org/downloads
1. Exome Data
2. Genome Data
Usually we think of gnomAD as a collection of germ cell mutations, which can be used as a reference when studying somatic mutations. Although some possible somatic mutation sites have been kicked out as much as possible in the process of database construction, there will still be some, and frequency filtering can be considered at this time.
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