GSCAN PheWeb Documentation

How to install PheWeb

To install PheWeb, follow this link

To import datasets

1. Edit pheno-list.json file, include the association files that need to be imported.
   
2. Download the datafiles, make sure the column names are valid.
3. Load the association files by running -- pheweb process

Things need to be considered

1. When you load your association files, PheWeb will automatically initiate the jobs to download necessary files, make sure you have enough disk space.
2. If you have multiple association files, the loading process could take hours.
3. If there is a new dataset needs to be added, after adding it into the json file, we will need to ask IT to run pheweb process on genome2.cla.umn.edu.

The file must have columns for:

column description	name	other allowed column names	allowed values
chromosome	chrom	#chrom, chr	1-22, X, Y, M, MT, chr1, etc
position	pos	beg, begin, bp	integer
reference allele	ref	reference	must match reference genome
alternate allele	alt	alternate	anything
p-value	pval	pvalue, p, p.value	number in [0,1]

You may also have columns for:

column description	name	other allowed column names	allowed values
minor allele frequency	maf		number in (0,0.5]
allele frequency	af	a1freq, frq	number in (0,1)
AF among cases	case_af	af.cases	number in (0,1)
AF among controls	control_af	af.controls	number in (0,1)
allele count	ac		integer
effect size	beta		number
standard error of effect size	sebeta	se	number
odds ratio	or		number
R2	r2		number
number of samples	num_samples	ns, n	integer, must be the same for every variant in its phenotype
number of controls	num_controls	ns.ctrl, n_controls	integer, must be the same for every variant in its phenotype
number of cases	num_cases	ns.case, n_cases	integer, must be the same for every variant in its phenotype