Metaxcan Web Application needs users to enter information concerning the format of the GWAS input files.

Here are some examples of how to describe them, based on some common GWAS data.

Bear in mind that MetaXcan needs to figure out the Z-score of GWAS betas; so, it would need a p-value and either of the following: beta, beta sign, or odd ratio.

Plink assoc files

These GWAS files are gzip compressed and have a header and look similar to:

         SNP  A1  A2     FRQ    INFO    BETA      SE       P
    rs940550   C   T  0.1522  0.9890 2985.6704 2857.8777   0.299
   rs6650104   A   G  0.0000  0.0000      NA      NA      NA
...
...

In order for MetaXcan to be able to parse the file, a user needs to specify BETA columns and P columns.

Parameter	Value	explanation
P-Value Column Name	P
Beta Column Name	BETA
SNP Column Name	SNP	Default UI value
Other Allele Column Name	A1	Default UI value
Effect Allele Column Name	A2	Default UI Value
Files Are GZip Compressed	Checked
Column Separator	Any Whitespace

MAGIC consortium.

Suppose that a user has a GWAS set of gzipped files like Magic Consortium's.

snp     effect_allele   other_allele    maf     effect  stderr  pvalue
rs10    a       c       .123    1.23e-03 1.23e-02 .9999
....

Then, a user would have to set:

Parameter	Value	explanation
P-Value Column Name	pvalue
Beta Column Name	effect
SNP Column Name	snp
Other Allele Column Name	other_allele
Effect Allele Column Name	effect_allele
Files Are Gzip Compressed	Checked
Column Separator	Any Whitespace

Example CSV

Suppose now that a user has plain CSV files with the following information:

OrigSNPname,Chromosome,Position,Effect,Baseline,OR,SE,pvalue
rs58108140,1,10583,A,G,0.96099,0.08405,0.5265
...

Then, to parse the files, the following would have to be set:

Parameter	Value	explanation
P-Value Column Name	pvalue
Odd Ratio Column Name	OR
SNP Column Name	OrigSNPName
Other Allele Column Name	Baseline
Effect Allele Column Name	Effect
Files Are Gzip Compressed	Unchecked
Column Separator	Comma