Outputs

Haplotype file format

Discovered haplotypes will be written in a special .haps file format.

This is a tab-separated file composed of different types of lines. The first field of each line is a single, uppercase character denoting the type of line.

Type	Description
#	Comment
M	Metadata
H	Haplotype
V	Variant

# Comment line

Comment lines begin with # and are ignored.

M Metadata

Describes attributes of the file, itself, including the version of the format spec.

H Haplotype

Haplotypes contain the following attributes:

Column	Field	Type	Description
1	Haplotype ID	int	Identifies a haplotype within a tree; unique across other haplotypes in the tree
2	Tree ID	int	A unique identifier for the tree that this haplotype belongs to
3	Effect size	float	The effect size of the association between this haplotype and the trait
4	p-value	float	The p-value of the association between this haplotype and the trait
5	PIP	float	The posterior inclusion probability for the causality of this haplotype

V Variant

Variant lines must follow the haplotype to which they belong. They contain the following attributes:

Column	Field	Type	Description
1	Variant ID	string	The unique ID for this variant, as defined in the genotypes file
2	Haplotype ID	int	Identifies a haplotype within a tree; unique across other haplotypes in the tree
3	Tree ID	int	A unique identifier for the tree that this haplotype belongs to
4	Allele	bool	The allele of this variant within the haplotype
5	Score	float	The importance of including this variant within the haplotype