The gnomAD v2 tracks show variants from 125,748 exomes and 15,708 whole genomes, all mapped to
the GRCh37/hg19 reference sequence and lifted to the GRCh38/hg38 assembly. The data originate
from 141,456 unrelated individuals sequenced as part of various population-genetic and
disease-specific studies
collected by the Genome Aggregation Database (gnomAD), release 2.1.1.
Raw data from all studies have been reprocessed through a unified pipeline and jointly
variant-called to increase consistency across projects. For more information on the processing
pipeline and population annotations, see the following blog post
and the 2.1.1 README.
gnomAD v2 data are based on the GRCh37/hg19 assembly. These tracks display the
GRCh38/hg38 lift-over provided by gnomAD on their downloads site.
The gnomAD MPC score (Missense Deleteriousness Prediction by Constraint) is available for now only on hg19.
For questions on the gnomAD data, also see the gnomAD FAQ.
Display Conventions and Configuration
The gnomAD v2.1.1 track follows the standard display and configuration options available for
VCF tracks, briefly explained below.
In mode, a vertical line is drawn at the position of
each variant.
In mode, "ref" and "alt" alleles are
displayed to the left of a vertical line with colored portions corresponding to allele counts.
Hovering the mouse pointer over a variant pops up a display of alleles and counts.
Filtering Options
Four filters are available for these tracks, the same as the underlying VCF:
AC0: Allele Count 0 after filtering out low confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls))
InbreedingCoeff: Inbreeding Coefficient < -0.3
RF: Used to exclude/include variants that failed Random Forest filtering thresholds of 0.055272738028512555, 0.20641025579497013 (probabilities of being a true positive variant) for SNPs, indels)
Pass: Variant passes all 3 filters
There are two additional filters available, one for the minimum minor allele frequency, and a configurable filter on the QUAL score.
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, and the genome annotations are stored in files that
can be downloaded from our download server, subject
to the conditions set forth by the gnomAD consortium (see below). Variant VCFs can be found in the
vcf/ subdirectory.
