Source data version: Release 2.1.1 Data last updated at UCSC: 2022-01-03 13:25:06
Description
The Genome Aggregation Database (gnomAD) - Genome and Exome Variants tracks
show single nucleotide variants (SNVs) and small insertion/deletion variants of <50 nucleotides
(indels) from 125,748 exomes and 15,708 whole genomes of unrelated individuals, short variant
release 2.1.1. For more information on the processing pipeline and population annotations, see the following
blog post and the
2.1.1 README.
There are two tracks making up this data set:
gnomAD Exome Variants: short variants of 125,748 exomes, release 2.1.1.
gnomAD Genome Variants: short variants of 15,708 genomes, release 2.1.1.
VCF files were downloaded according to the
gnomAD instructions and
transformed into one bigBed file per data set, as described in UCSC Methods.
Display Conventions and Configuration
Display conventions
By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters
described below), before the track switches to dense display mode.
Mouse hover on an item will display many details about each variant, including the affected gene(s),
the variant type, and annotation (missense, synonymous, etc).
Clicking on an item will display additional details on the variant, including a population frequency
table showing allele count in each sub-population.
Following the conventions on the gnomAD browser, items are shaded according to their Annotation
type:
pLoF
Missense
Synonymous
Other
Label Options
To maintain consistency with the gnomAD website, variants are by default labeled according
to their chromosomal start position followed by the reference and alternate alleles,
for example "chr1-1234-T-CAG". dbSNP rsID's are also available as an additional
label, if the variant is present in dbSnp.
Filtering Options
Three filters are available for these tracks:
FILTER: Used to exclude/include variants that failed Random Forest
(RF), Inbreeding Coefficient (Inbreeding Coeff), or Allele Count (AC0) filters. The
PASS option is used to include/exclude variants that pass all of the RF,
InbreedingCoeff, and AC0 filters, as denoted in the original VCF.
Annotation type: Used to exclude/include variants that are annotated as
Probability Loss of Function (pLoF), Missense, Synonymous, or Other, as
annotated by VEP version 85 (GENCODE v19).
Variant Type: Used to exclude/include variants according to the type of
variation, as annotated by VEP v85.
For gnomAD Exome Variants v2.1.1, there is a Non-cancer filter used to exclude/include variants
from samples of individuals who were not ascertained for having cancer in a cancer study.
As an individual variant can possess multiple FILTER and Variant Type values,
it is important to select any options of interest (or rather deselect if trying
to filter out variants from the display).
For the full steps used to create the track at UCSC, please see the section
denoted "gnomAD v2.1.1 update" in the hg19 makedoc.
Data Access
The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the
data may be queried from our REST API or downloaded as files from our
download server, subject to the conditions set forth by the
gnomAD consortium (see below). Please refer to our
mailing list archives for questions or our
Data Access FAQ
for more information.
More information about using and understanding the gnomAD data can be found in the
gnomAD FAQ site.