Am new to bioinformatics but not to hacking code. I'm working on an appllication and need some guidance on getting the data. I've read a few other posts and still the solution eludes me.
I want to generate the following data from GWAS
all chromosomes, chr 1-22,x,y
max pvalue 1.0
the size of the database doesn't matter. the application/database will be local as it may or may not have internet access to query.
i want an output in this form
Phenotype, SNP, pvalue chr#, start location, annotation
eventually i want to be able to link in a pharmacognetic database
here's one of the many variations i've tried
Chromosome : 1
Marker Start (bp): 1
Marker End (bp): 10000000
Greater or equal : -log > = 1
Phenotype Annotation Identifier
can someone help?