anchor.diff:  2. <<faq-B2,What can I type into the search bar?>>
   
   
  -3. <<faq-B3,What is the difference between a reported trait and a mapped trait?>>
  -
  -
  -4. <<faq-B4,Can I limit my search to a specific type of field such as author?>>
  -
  -
  -5. <<faq-B5,What is the difference between the blue links and link-out icons?>>
  -
  -
  -6. <<faq-B6,When I search for a certain trait why are other traits returned?>>
  -
  -
  -7. <<faq-B7,Can I search for multiple or compound traits?>>
  -
  -
  -8. <<faq-B8,Why did my search return no results even though I am sure there used to be a trait like this in the Catalog?>>
  -
  -
  -9. <<faq-B9,How do I search for ancestry data in the GWAS Catalog?>>
  -
  -
  -10. <<faq-B10,Can I search by genomic region?>>
  -
  -
  -11. <<faq-B11,How do I identify interaction studies in the GWAS Catalog?>>
  -
  -
  -12. <<faq-B12,How can I search for targeted and exome array studies and associations?
  ->>
  +3. <<faq-B3,Can I limit my search to a specific type of field such as author?>>
  +
  +
  +4. <<faq-B4,Can I search by genomic region?>>
  +
  +
  +5. <<faq-B5,How can I identify variants in linkage disequilibrium (LD) with a variant?>>
  +
  +
  +6. <<faq-B6,What is the difference between the blue links and link-out icons?>>
  +
  +
  +=== B(i). Searching by trait
  +
  +1. <<faq-B7,What is the difference between a reported trait and a mapped trait?>>
  +
  +
  +2. <<faq-B8,When I search for a certain trait why are other traits returned?>>
  +
  +
  +3. <<faq-B9,How are multiple or compound traits represented in the Catalog?>>
  +
  +
  +4. <<faq-B10,Can I search for associations with more than one trait at the same time?>>
  +
  +
  +5. <<faq-B11,Why did my search return no results even though I am sure there used to be a trait like this in the Catalog?>>
  +
  +
  +=== B(ii). Searching for interaction and pleiotropy studies
  +
  +1. <<faq-B12,How do I identify interaction studies in the GWAS Catalog?>>
  +
  +
  +2. <<faq-B13,How do I identify pleiotropy studies in the GWAS Catalog?>>
   
   
   === C. Filters
  
positive.code: 
  '''
  
  _Last updated: 19 September 2017_
  
negative.code: 
  6. <<faq-E6,Why do the counts in the legend do not always match the association count for a search?>>
  
  === F. Genomic mappings and annotation
  
  1. <<faq-F1,How is the genomic annotation for each SNP provided?>>
  
  2. <<faq-F2,What is the difference between the old (pre-2016?) and the new mapping/annotation pipeline?>>
  
  3. <<faq-F3,Which genome build is the Catalog on?>>
  
  4. <<faq-F4,How can I access the GWAS Catalog data on alternative genome builds?>>
  
  5. <<faq-F5,Why do some SNPs not have any corresponding mapping information?>>
  
  6. <<faq-F6,How are SNP-SNP interactions and multi-SNP haplotypes displayed and annotated?>>
  
  
  === G. Ancestry
  
  1. <<faq-G1,How is the ancestry data in the GWAS Catalog provided?>>
  
  2. <<faq-G2,How do I search for ancestry data in the GWAS Catalog?>>
  
  3. <<faq-G3,What does the "Pre-2011 ancestry not double-curated" flag next to some of the ancestry data mean?>>
  
  4. <<faq-G4,Why is the ancestry information provided in a separate downloadable spreadsheet to the rest of the study-level information?>>
  
  
  
  === H. Programmatic access
  
  1. <<faq-H1,Is there a way of programmatically retrieving data from the GWAS Catalog?>>
  
  2. <<faq-H2,How do I use the GWAS Catalog REST API?>>
  
  
  === I. Summary Statistics
  
  1. <<faq-I1,How do I find out which publications have full summary statistics available?>>
  
  2. <<faq-I2,I am an author and would like to deposit my summary statistics in the GWAS Catalog, how to I go about this?>>  
  
  
  
  '''
  == A. General
  
  
  ==== [[faq-A1]]1. Why has the Catalog moved from the NHGRI to the EBI?
  
  From September 2010 to the present, delivery and development of the Catalog has been a collaborative project between EMBL-EBI and NHGRI. In March 2015 the Catalog infrastructure moved to EMBL-EBI to enable delivery of an improved user interface, including ontology driven Catalog searching, and new curatorial infrastructure, supporting improved QC processes. Content available from the http://www.genome.gov/gwastudies/[NHGRI site] was last updated 20 February 2015 and is now frozen. Updated content is available from http://www.ebi.ac.uk/gwas/[here]. The latest updated download file is now available from link:../api/search/downloads/full[here].
  
  ==== [[faq-A2]]2. How can I learn more about using the GWAS Catalog?
  
  Have a look at our link:related-resources[Related Resources] page for training materials, or see the <<B,FAQ sections below>> for some hints and tips.
  
  ==== [[faq-A3]]3. How can I stay informed about new search features and developments?
  
  You can subscribe to our announcement list by sending an e-mail to gwas-announce-join@ebi.ac.uk with subject heading "subscribe". Traffic on this list will be limited to important announcements only so you don't need to worry about getting bombarded with loads of emails. For queries and user discussion, we have separate mailing lists, gwas-info@ebi.ac.uk to contact the Catalog team and gwas-users@ebi.ac.uk for user discussion (subscribe by emailing gwas-users-join@ebi.ac.uk with subject heading "subscribe"). You can also follow us on Twitter https://twitter.com/GWASCatalog[@GWASCatalog].
  
  ==== [[faq-A4]]4. How should I cite the GWAS Catalog?
  
  Please see the link:about[About] page for citation guidance.
  
  ==== [[faq-A5]]5. What are the terms and conditions for accessing the GWAS Catalog data and code?
  
  The GWAS Catalog data can be used under the standard terms of use for EBI services which can be found at http://www.ebi.ac.uk/about/terms-of-use. Our code is available under the http://www.apache.org/licenses/LICENSE-2.0[Apache version 2.0 license]
  
  ==== [[faq-A6]]6. How often are the GWAS Catalog and diagram updated?
  
  New data is added to the GWAS Catalog and diagram on a weekly basis, with new data generally going public every Tuesday. Data releases include all downloadable spreadsheets.
  
  ==== [[faq-A7]]7. Why does the data I just downloaded look different from what I downloaded in the old NHGRI Catalog?
  
  Due to the way we now process the Catalog data for the full download, you may find that your spreadsheet has more rows than it did previously. There should be no other major differences between the old and new spreadsheets but if you find any issues or inconsistencies, please do not hesitate to contact the GWAS Catalog team at gwas-info@ebi.ac.uk.
  
  ==== [[faq-A8]]8. What happened to the "CNV" annotation in the interface?
  
  Studies looking at copy number variations (CNV) are not part of the remit of the GWAS Catalog. Historically, a couple of CNV studies had been included in the Catalog but these have now been removed. As the Catalog no longer contains any CNV studies, the decision was made to also eliminate the CNV flag from the search results for studies. The corresponding column is still available in the downloadable full Catalog spreadsheet to preserve backwards compatibility with previous spreadsheet versions.
  
  
  ==== [[faq-A9]]9. A new GWAS study has just been published. Why is it not in the GWAS Catalog?
  
  Due to the considerable manual curation effort that goes into each study in the GWAS Catalog, it takes a while for studies to be published in the Catalog after they have been first indexed in Pubmed. As the complexity of studies in terms of study design and statistical analysis of results continues to increase, so does the curation effort required to extract the correct information in line with our extraction guidelines. The GWAS Catalog curation team work as fast as they can to process studies while maintaining the high standard of accuracy our users expect of the Catalog. We are in the process of trialling various approaches to speed up the curation process.
  
  ==== [[faq-A10]]10. Where can I find the GWAS Catalog infrastructure code?
  
  All our code is freely available from https://github.com/EBISPOT/goci[our Github repository].
  
  
  ==== [[faq-A11]]11. Why is there sometimes more than one Catalog entry for the same publication?
  
  Some publications are split into multiple GWAS Catalog entries, if more than one GWAS has been included in a publication, with distinct traits, sample cohorts or other unique characteristics. You can read more about how we curate publications containing multiple analyses in our link:methods[ Methods] section. Each entry or "GWAS Catalog study" has a stable accession number which is linked to the publication-level information.
  
  ==== [[faq-A12]]12. How do I find out the accession id for my study of interest?
  
  Each separate study in the GWAS Catalog has an accession id beginning with “GCST”. Prior to March 2018, this was only available in the Studies download files. Study accessions are now visible in the web interface, in the Studies table, under the column heading “study accession”.  Accession numbers are included in the v1.0.1 spreadsheets for associations and studies as well the ancestry spreadsheets. Accession numbers are not provided in the v1.0 spreadsheets as these are legacy formats provided only to support backwards compatibility with the old NHGRI spreadsheet.
  
  
  == [[B]]B. Exploring the GWAS Catalog data
  
  ==== [[faq-B1]]1. How do I do a search?
  
  Type your query, e.g. “breast cancer”, into the search box and hit return or click the search icon.
  
  ==== [[faq-B2]]2. What can I type into the search bar?
  
  You can type any text you wish into the search bar. This will then return any exact string matches within a number of data fields in the Catalog, including title, author, journal, reported trait, mapped (ontology) trait, mapped trait's synonyms, mapped trait's parents, sample descriptions, genes and SNPs. 
  
  ==== [[faq-B3]]3. Can I limit my search to a specific type of field such as author?
  
  At the moment, the main search only supports searching across all fields, so if your search term is for example "Parkinson", you will see results for Parkinson’s disease as well as studies with an author named Parkinson. Note that since March 2018, all authors associated with a publication are included in our database, so searching for an author name will return all studies featuring that author, not only first author publications.
  To identify all first author publications by an individuals, sort the search results by Author name, using the arrows at the top of the Author column. If you would like to search for a specific study, you can search by Pubmed ID.
  To limit your search to a specific trait or set of traits, we would suggest doing a general search for that trait first, then filtering your results using the <<Filters,trait filter>> dropdown to the left of the search results. For example, following a search for "lupus", you can limit your search results to "Systemic lupus erythematosus" via the dropdown.
  We are working on an "advanced search" mode where you can limit your search to certain fields or search for specific combinations of fields. To be alerted as soon as this functionality becomes available, subscribe to our <<faq-A2,announcement list>>.
  
  ==== [[faq-B4]]4. Can I search by genomic region?
  
  You can search by genomic region using the format chromNumber:bpLocation-bpLocation, for example 6:16000000-25000000. Please note that this search returns only results of type "Association".
  
  ==== [[faq-B5]]5. How can I identify variants in linkage disequilibrium (LD) with a variant?
  
  LD calculation between a variant of interest and its surrounding variants can be accessed programmatically using the Ensembl REST API (http://rest.ensembl.org/documentation/info/ld_pairwise_get) where you can specify a variant ID, a window size of the region surrounding the variant, a population and a cut-off for the calculation results.
  In case of a dataset with more than 1 variant of interest, several independant calls to the Ensembl REST API (http://rest.ensembl.org/documentation/info/ld_pairwise_get) can be done. Variants in LD with a specific GWAS Catalog variant can also be visualised on our new prototype variant page http://www.ebi.ac.uk/gwas/beta/variants.
  
  ==== [[faq-B6]]6. What is the difference between the blue links and link-out icons?
  Clicking on a term highlighted in blue (e.g. author, trait or rsID) performs a full new search for this term. Clicking on a little link-out icon next to a term takes you to an external page related to this term, e.g. Pubmed Central for studies or Ensembl for SNPs or genes.
  
  == B(i). Searching by trait
  
  ==== [[faq-B7]]1. What is the difference between a reported trait and a mapped trait?
  Each study is assigned a trait description that best represents the phenotype under investigation. This is known as the reported trait as it is taken from the study publication. All reported traits are mapped to terms from the http://www.ebi.ac.uk/efo[Experimental Factor Ontology] resulting in one or more mapped traits. For more information about how ontologies are used in the catalog, see our link:ontology[ontology] page.
  
  ==== [[faq-B8]]2. When I search for a certain trait why are other traits returned?
  The search algorithm searches across a number of fields including study titles, sample descriptions, reported traits, mapped (ontology) traits, mapped traits' synonyms and mapped traits' parents. If your search term is a match to any of these categories, that result will be returned. If you search for "metabolic disease" for example, you will see a number of reported traits mapped to ontology traits such as "type II diabetes mellitus" because metabolic disease is a parent of diabetes in the ontology. Equally, searching for "diabetes" will return some potentially unexpected results as the search returns studies that were carried out in a sample population of diabetics, so the term "diabetes" is matched in the sample description. Filtering via the trait dropdown allows you to exclude unwanted traits for now and a more refined "advanced search" mode is under development.
  
  ==== [[faq-B9]]3. How are multiple or compound traits represented in the Catalog?
  
  Where a study includes cases and controls all sharing a background trait, this is indicated by the use of the word “in” in the reported trait. For example, if drug responders with bipolar disorder were compared to drug non-responders with bipolar disorder, the reported trait would be "drug response in bipolar disorder”. 
  
  Where a study has combined groups of individuals with different traits in the same analysis, this is indicated by the use of the word “or” in the reported trait. For example, if individuals with bipolar disorder and individuals with schizophrenia were compared to controls in the same analysis, the reported trait would be "bipolar disorder or schizophrenia”. 
  
  Where a study includes individuals each having multiple traits, this is indicated by the word “and” in the reported trait. For example, if individuals diagnosed with bipolar disorder who show binge-eating behaviour were compared to controls, the reported trait would be “bipolar disorder and binge eating”.
  
  See also <<faq-B13,How do I identify pleiotropy studies in the GWAS Catalog?>>
  
  
  ==== [[faq-B10]]4. Can I search for associations across more than one trait at the same time?
  
  True multiple trait searching is currently not possible. The search bar searches for the exact text match of the search term entered within a range of Catalog fields, along with any related traits through the mapped ontology fields. For now, we would recommend searching by a more general trait, e.g. "schizophrenia", then selecting any desired compound traits from the trait filter dropdown e.g. “Bipolar disorder and schizophrenia”, “Schizophrenia or bipolar disorder”. Alternatively the data download enables complex analysis. We are working to improve this feature of the search in the near future. You can view our prototype trait-based search page at  http://www.ebi.ac.uk/gwas/beta/efotraits, which allows easy visualization of all associations with a trait, or combinations of multiple traits.
  
  ==== [[faq-B11]]5. Why did my search return no results even though I am sure there used to be a trait like this in the Catalog?
  Our search functionality is currently unable to allow for typos or term variations, so if you accidentally type "beast cancer" instead of "breast cancer", you will not get any results. Equally, "metabolic disorder" won't return any results while "metabolic disease" will return loads. A browseable list of all reported traits is available link:http://www.ebi.ac.uk/gwas/search/traits[here] and autocomplete functionality for the search box is coming soon. In the mean time, if you get stuck, we recommend varying your search term or searching for your term in http://www.ebi.ac.uk/efo[EFO] to get an idea of what other terms might be available.
  
  
  
  == B(ii). Searching for interaction and pleiotropy studies
  
  
  ==== [[faq-B12]]1.How do I identify interaction studies in the GWAS Catalog?
  
  The GWAS Catalog contains SNP-by-SNP and SNP-by-environment interaction studies as long as the SNPs analysed meet our criteria of being genome-wide (see www.ebi.ac.uk/gwas/docs/methods). For both types of study, the term “interaction” is added in parenthesis to the reported trait. For SNP-by-environment interaction studies, the environmental component is also included in the reported trait e.g. “Lung cancer (smoking interaction)” or “Bone mineral density (gender interaction)”. For SNP-by-SNP interaction studies the term “SNP x SNP interaction” is added in parenthesis.
  To identify interaction studies, you can search for “interaction” in both the GWAS Catalog search and the download spreadsheet.
  
  ==== [[faq-B13]]2. How do I identify pleiotropy studies in the GWAS Catalog?
  
  Studies aimed at identifying pleiotropic SNP associations have the term “pleiotropy” added in parenthesis to the reported trait, together with all traits investigated, e.g. “Schizophrenia or lung cancer (pleiotropy). To identify all pleiotropy studies, you can search for “pleiotropy” in both the GWAS Catalog search and the download spreadsheet.
  
  
  
  
  
  
  == C. [[Filters]]Filters
  
  ==== [[faq-C1]]1. How do I filter my results by p-value?
  To filter association results by p-value, enter a maximum p-value into the appropriate filter box. The input format is "mantissa"x 10^"exponent"^, e.g. 5 x 10^-8^.
  