The gwasCatalog is NHGRI's collection of Genome-Wide Association (GWA) Studies SNPs. We downloaded the data for this annotation source from the UCSC Genome Browser database (http://genome.ucsc.edu/cgi-bin/hgTables?command=start). You can use this annotation source as a position, range or field-based annotation source. Examples for usage as a range-based and field-based annotation source are given on this page. (By default the usage for this annotation source is a position-based annotation source).

1.  Usage

Here are the available gwasCatalog fields for annotation and filtering.

vtools show annotation gwasCatalog -v2
Annotation database gwasCatalog (version hg19_20140112)
Description:            This database contains single nucleotide polymorphisms
  (SNPs) identified by published Genome-Wide Association Studies (GWAS),
  collected in the Catalog of Published Genome-Wide Association Studies at the
  National Human Genome Research Institute (NHGRI). From
  http://www.genome.gov/gwastudies/:
Database type:          position
Number of records:      18,027
Distinct positions:     13,980
Reference genome hg19:  chr, position

Field:                  chr
Type:                   string
Missing entries:        0
Unique Entries:         36

Field:                  position
Type:                   integer
Comment:                one-based position in chromosome
Missing entries:        0
Unique Entries:         13,974
Range:                  5641 - 249168436

Field:                  name
Type:                   string
Comment:                ID of SNP associated with trait
Missing entries:        0
Unique Entries:         12,003

Field:                  pubMedId
Type:                   integer
Comment:                PubMed ID of publication of the study
Missing entries:        0
Unique Entries:         1,488
Range:                  15761122 - 23894747

Field:                  author
Type:                   string
Comment:                First author of publication
Missing entries:        0
Unique Entries:         1,129

Field:                  pubDate
Type:                   string
Comment:                Date of publication
Missing entries:        0
Unique Entries:         899

Field:                  journal
Type:                   string
Comment:                Journal of publication
Missing entries:        0
Unique Entries:         204

Field:                  title
Type:                   string
Comment:                Title of publication
Missing entries:        0
Unique Entries:         1,488

Field:                  trait
Type:                   string
Comment:                Disease or trait assessed in study
Missing entries:        0
Unique Entries:         865

Field:                  initSample
Type:                   string
Comment:                Initial sample size
Missing entries:        0
Unique Entries:         1,579

Field:                  replSample
Type:                   string
Comment:                Replication sample size
Missing entries:        0
Unique Entries:         1,064

Field:                  region
Type:                   string
Comment:                Chromosome band / region of SNP
Missing entries:        0
Unique Entries:         871

Field:                  genes
Type:                   string
Comment:                Reported gene(s)
Missing entries:        0
Unique Entries:         6,521

Field:                  riskAllele
Type:                   string
Comment:                Strongest snp-risk allele
Missing entries:        0
Unique Entries:         12,631

Field:                  riskAlFreq
Type:                   string
Comment:                risk allele frequency
Missing entries:        0
Unique Entries:         1,661

Field:                  pValue
Type:                   float
Comment:                p-Value
Missing entries:        0
Unique Entries:         623
Range:                  0 - NS

Field:                  pValueDesc
Type:                   string
Comment:                p-Value description
Missing entries:        0
Unique Entries:         1,563

Field:                  orOrBeta
Type:                   string
Comment:                Odds ratio or beta
Missing entries:        0
Unique Entries:         863

Field:                  ci95
Type:                   string
Comment:                95% confidence interval
Missing entries:        0
Unique Entries:         5,604

Field:                  platform
Type:                   string
Comment:                Platform and [SNPs passing QC]
Missing entries:        0
Unique Entries:         1,279

Field:                  cnv
Type:                   string
Comment:                Y if copy number variant
Missing entries:        0
Unique Entries:         1

2.  Details

2.1  gwasCatalog: usage as a position-based annotation source (default)

To check if your variants contain any gwas hits, you can

vtools use gwasCatalog
vtools select variant "gwasCatalog.chr is not NULL" -t gwasHits

However, because GWA studies use tagging SNPs to identify associated (hopefully) causal variants, your dataset might not contain the exact SNP that is reported in gwas catalog. It might contains the casual variant or other associations that are in vicinity (in LD) with the reported gwas hits. Therefore, it make more sense to find variants that are close to the reported gwas hits.

2.2  gwasCatalog: usage as a range-based annotation source

The most flexible way to use this annotation source is to link your variants to GWA hits with a position range. The following links your variant positions to GWA hits using variant chromosomal locations that are +/- 5000bp within the GWA hit.

vtools use gwasCatalog --anno_type range --linked_fields chr position-5000 position+5000

Then you can generate a useful report showing what known gwas hits are near your variants. The following command generates a report showing Type 2 diabetes hits near your variants.

vtools select variant "gwasCatalog.trait == 'Type 2 diabetes'" -o variant.chr variant.pos variant.ref variant.alt 
 gwasCatalog.trait gwasCatalog.name gwasCatalog.position gwasCatalog.pValue gwasCatalog.journal
 gwasCatalog.title > variants_near_diabetes_gwas_hits.txt
1       207653395       C       A       Type 2 diabetes rs17045328      207652176       7e-06   PLoS Genet      Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from Southeast Asia.
11      17408630        C       T       Type 2 diabetes rs5215  17408630        4e-07   Nat Genet       Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
11      17408630        C       T       Type 2 diabetes rs5215  17408630        5e-11   Science Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes.
11      17408630        C       T       Type 2 diabetes rs5219  17409572        1e-07   Science Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.
11      17408630        C       T       Type 2 diabetes rs5219  17409572        1e-09   Diabetes        Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data.
11      17408630        C       T       Type 2 diabetes rs5219  17409572        5e-07   Diabetes        Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data.
11      17408630        C       T       Type 2 diabetes rs5219  17409572        7e-11   Science A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.
11      17409069        G       A       Type 2 diabetes rs5215  17408630        4e-07   Nat Genet       Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
11      17409069        G       A       Type 2 diabetes rs5215  17408630        5e-11   Science Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes.
11      17409069        G       A       Type 2 diabetes rs5219  17409572        1e-07   Science Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.
11      17409069        G       A       Type 2 diabetes rs5219  17409572        1e-09   Diabetes        Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data.
11      17409069        G       A       Type 2 diabetes rs5219  17409572        5e-07   Diabetes        Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data.
11      17409069        G       A       Type 2 diabetes rs5219  17409572        7e-11   Science A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.
11      17409572        T       C       Type 2 diabetes rs5215  17408630        4e-07   Nat Genet       Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
11      17409572        T       C       Type 2 diabetes rs5215  17408630        5e-11   Science Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes.
11      17409572        T       C       Type 2 diabetes rs5219  17409572        1e-07   Science Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.
11      17409572        T       C       Type 2 diabetes rs5219  17409572        1e-09   Diabetes        Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data.
11      17409572        T       C       Type 2 diabetes rs5219  17409572        5e-07   Diabetes        Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data.
11      17409572        T       C       Type 2 diabetes rs5219  17409572        7e-11   Science A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.
12      51354803        C       T       Type 2 diabetes rs12304921      51357542        7e-06   Nature  Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
15      91524841        G       T       Type 2 diabetes rs8042680       91521337        2e-10   Nat Genet       Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
15      91525197        C       T       Type 2 diabetes rs8042680       91521337        2e-10   Nat Genet       Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
4       6302519 G       A       Type 2 diabetes rs1801214       6303022 3e-08   Nat Genet       Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
4       6302707 C       T       Type 2 diabetes rs1801214       6303022 3e-08   Nat Genet       Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
4       6303022 C       T       Type 2 diabetes rs1801214       6303022 3e-08   Nat Genet       Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
4       6303354 G       A       Type 2 diabetes rs1801214       6303022 3e-08   Nat Genet       Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
4       6303955 G       A       Type 2 diabetes rs1801214       6303022 3e-08   Nat Genet       Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
.....

2.3  gwasCatalog: usage as a field-based annotation source

In this usage, you can annotate your variants with published GWA hits that are in the same cytoband as your project variants. You can link your variants to the cytoBand annotation source and then annotate your variant cytoBands to published GWA hits

vtools use cytoBand
vtools use gwasCatalog --anno_type field --linked_fields region --linked_by 'cytoBand.name'

Then you can generate a useful report showing what known gwas hits are in the same cytobands as your variants. Once again, the following command generates a report showing Type 2 diabetes hits near your variants - except this time "near" means GWA hits that are within the same cytoband as your variants.

vtools select variant "gwasCatalog.trait == 'Type 2 diabetes'" -o variant.chr variant.pos variant.ref variant.alt
  gwasCatalog.trait gwasCatalog.name gwasCatalog.position gwasCatalog.pValue gwasCatalog.journal
  gwasCatalog.title > variants_near_diabetes_gwas_hits.txt
1       117841245       C       T       Height  rs17038182      118868405       5e-07   Nat Genet       A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits.
1       117841245       C       T       Height  rs12735613      118883973       4e-11   Nat Genet       Genome-wide association analysis identifies 20 loci that influence adult height.
1       117841245       C       T       Waist-hip ratio rs984222        119503843       9e-25   Nat Genet       Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.
1       117841245       C       T       Type 2 diabetes rs10923931      120517959       4e-08   Nat Genet       Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
1       117847270       A       G       Height  rs17038182      118868405       5e-07   Nat Genet       A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits.
1       117847270       A       G       Height  rs12735613      118883973       4e-11   Nat Genet       Genome-wide association analysis identifies 20 loci that influence adult height.
1       117847270       A       G       Waist-hip ratio rs984222        119503843       9e-25   Nat Genet       Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.
1       117847270       A       G       Type 2 diabetes rs10923931      120517959       4e-08   Nat Genet       Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
.....