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GWAS data
Jonathan Hess edited this page Jul 21, 2017
·
10 revisions
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:
- Single nucleotide polymorphism (SNP) matching 1000 Genome rsIDs (
--snp-field
) - P-value (
---clump-field
)
FLEET will automatically run Plink's --clump
algorithm across chromosomes 1-22. It will use the following parameters by default.
--clump-p1 1.0
--clump-p2 1.0
--clump-r2 0.1
--clump-kb 1000
Reference data from the 1000G will be automatically pre-pruned for variants in high LD using the --indep
algorithm from Plink
:
--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:
--filter-founders
--maf 0.01
--geno 0.05
--mind 0.05
--hwe 1e-06
Grackle got no boss