Datasets

Description of datasets

Phenotypic

Genotypic

• Affy AXIOM snpchip (PLINK ped/map)

• Illumina OMNIexpress snpchip (PLINK ped/map)

• Exome Sequence (Fastq/Bam/VCF)

• Whole Genome Sequence - Low Coverage (Fastq/Bam/VCF)

Summary Level

There is a curated set of summary level GWAS statistics on the server

Path: /Volumes/archive/merrimanlab/central_datasets/summary_gwas

They are organised by trait and then by author/paper and follow this directory struture:

author_year/

• raw/
• cleaned/
• snptracker/
• plots/
• author_year.pdf
• author_year.bib
• README

Each study has a README that contains important information. Including as URL, date downloaded, genome build, citation information, and modifications to the data.

raw/

• contains the original data

cleaned/

• contains a 'cleaned' version of the data (tab separated, selected columns, etc.)
• reported as GRCh37 (hg19) co-ordinates

snptracker/

• contains the data annotated with marker/position from the SNPtracker program

The current available datasets include

Trait	Paper
Gout	Kottgen et al 2013
Gout	Merriman - ACR conference 2017
Gout	Merriman - ECN conference 2018
Urate	Kottgen et al 2013
Urate	Kanai et al 2018