Make a text file with these details for each haplotype:
- sample: this allows you to identify a haplotype with a particular sample, or to give it a name of your chosing. Must not exceed 10 characters or contain spaces.
- haplotype: this is the list of alleles that make up the haplotype, with no spaces
- freq: this is haplotype frequency which you can represent in various ways (see below)
- each haplotype is listed on a new line
- the first line gives the fieldnames in this order: sample, haplotype, freq
- the fields are separated by tabs
As shown in the examples below, you can choose how to represent haplotype frequency. One way is to list every sample separately, so that haplotypes present in several samples are listed several times: in that case put freq=1 to denote the fact that each line represents a single sample. Another way is to combine samples that have the same haplotypes: for freq give either the number of samples with that haplotype (eg 21) or their frequency within the population (eg 0.14).
Example 1: unique haplotypes with frequencies
sample haplotype freq
hap1 11111111111 0.35
hap2 11222222211 0.3
hap3 11111222222 0.2
hap4 11222221111 0.1
hap5 22222222222 0.05
Example 2: unique haplotypes with number of times each has been observed
sample haplotype freq
hap1 11111111111 35
hap2 11222222211 30
hap3 11111222222 20
hap4 11222221111 10
hap5 22222222222 5
Example 3: individual samples (each sample is a single chromosome)
sample haplotype freq
Jim_chr1 11111111111 1
Jim_chr2 11222222211 1
Mandy_chr1 11111222222 1
Mandy_chr2 11222221111 1
Angus_chr1 22222222222 1
Angus_chr2 11222222211 1
Don't worry if the columns don't line up nicely (this will depend on your text editor) as long as there's a single tab between each field.
