1. Using TASSEL
Getting TASSEL

4. Sequence Hapmap data format
Hapmap is a text based file format for storing sequence data.
Information on the SNPs as well as germplasm/lines/varities are stored in one file.
The first row contains the header labels, and each additional row contains all information associated with a single snp.
The first 11 columns described the attributes of the SNP. Genotypes start from The 12th column.
Not all positions should be filled for TASSEL to read the data except chrom and pos
TASSEL to correctly read Hapmap data, the data must be in order of position within each chromosome/contigs.
The file should be TAB delimited format

6. Numeric Data
Used for trait and covariate data such as population structure.
Consists of two parts: a header that defines data structure and a body containing the main data.
Tabs should be used as delimiters.
Trait format starts with <Trait> followed by names of columns
Covariate format starts with <Covariate> followed by names of columns.
<Trait>
Height
Yield
AGFD_1 56
1000
AGFD_2 67
1300
AGFD_3 66
800
AGFD_4 44
1250
AGFD_5 23
500
AGFD_6 85
1782
AGFD_7 78
1299
AGFD_8
1982
AGFD_9
2011
AGFD_10 89
600

7. Phenotype data <Trait> Seed_Lg Seed_W Seed_T Seed_100WT
Yield_kgha A1
4.85 A2
177
4.38 A3
5.545
4.13 A4 A5 A6
3.805 A7
990.27 A8 A9
5.015
A10
5.86
9.785
A11
14.925
A12
210.5
5.525
11.02
A13
4.805
10.995
A14
A15
5.81
4.95
A16
4.625
11.935
A17
152.5
6.005
4.495
830.62
A18
11.38
A19
107.5
5.03
A20
99.5
5.885
4.83
A21

8. File load data

9. Sort genotype

10. Load data after sorting

11. Filter menu

13. Site name filter

14. Taxa Filter

15. Filter Taxa by Properties