Causal SNPs

You can specify causal SNPs in a tab-delimited .snplist file. We follow GCTA’s .snplist format for this type of file. It has just two columns:

Name	Type	Description
ID	string	A unique identifier for this variant in the file (ex: ‘rs1234’)
BETA	float	The effect size assigned to this variant (ex: 0.08)

Note

You should not include a header in this file. The file format does not have one.

Examples

Refer to tests/data/apoe.snplist for an example containing just two SNPs.

rs429358        0.73
rs7412  0.30

Converting to a .hap file

The capabilities of the .snplist format are limited. For example, it does not allow users to specify a causal allele (REF vs ALT) for each SNP. You can use the haptools API to upgrade to a .hap file if needed.