GWAS data

What data does FLEET accept?

It is expected that you will be analyzing a file of genome-wide association study (GWAS) summary statistics. This file should have at least two columns:

1. Single nucleotide polymorphism (SNP) matching 1000 Genome rsIDs (--snp-field)
2. P-value (---clump-field)

FLEET will automatically run Plink's --clump algorithm across chromosomes 1-22. It will use the following parameters by default.

1. --clump-p1 1.0
2. --clump-p2 1.0
3. --clump-r2 0.1
4. --clump-kb 1000

Reference data from the 1000G will be automatically pre-pruned for variants in high LD using the --indep algorithm from Plink:

1. --maf .05 --indep 100 5 2

Note that CEUqc_1kg_phase1_* reference data were originally downloaded from the Plink resources page. I extracted samples corresponding to the CEU population, and implemented the following quality control measures:

1. --filter-founders
2. --maf 0.01
3. --geno 0.05
4. --mind 0.05
5. --hwe 1e-06

Example GWAS data

https://www.med.unc.edu/pgc/results-and-downloads