This is a test version of Biostars. For the public version, visit https://www.biostars.org.
About the item name of UCSC GWAS catalog

I got the GWAS catalog data from the UCSC link below, but I don't know what each column is for. https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gwasCatalog.txt.gz

Also, the description of the following link doesn't say anything, so if there is anything else I should look at, I would appreciate it if you could let me know.

https://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=phenDis&hgta_track=gwasCatalog&hgta_table=gwasCatalog&hgta_doSchema= describe+table+schema

ucsc gwas catalog
• 1,264 views • link
written by ayasu • ayasu

1 answer

https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gwasCatalog.sql

  `bin` smallint(5) unsigned NOT NULL,
  `chrom` varchar(255) NOT NULL,
  `chromStart` int(10) unsigned NOT NULL,
  `chromEnd` int(10) unsigned NOT NULL,
  `name` varchar(255) NOT NULL,
  `pubMedID` int(10) unsigned NOT NULL,
  `author` varchar(255) NOT NULL,
  `pubDate` varchar(255) NOT NULL,
  `journal` varchar(255) NOT NULL,
  `title` varchar(1024) NOT NULL,
  `trait` varchar(255) NOT NULL,
  `initSample` longblob NOT NULL,
  `replSample` longblob NOT NULL,
  `region` varchar(255) NOT NULL,
  `genes` longblob NOT NULL,
  `riskAllele` longblob NOT NULL,
  `riskAlFreq` varchar(255) NOT NULL,
  `pValue` varchar(255) NOT NULL,
  `pValueDesc` varchar(255) NOT NULL,
  `orOrBeta` varchar(255) NOT NULL,
  `ci95` varchar(255) NOT NULL,
  `platform` varchar(255) NOT NULL,
  `cnv` enum('Y','N') NOT NULL,
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks for the details you provided. I will try to process the data with your reference.

• 0 views • link
written by ayasu • ayasu

Log in to answer this question.

More posts like this