Upload files to use GAMMA-RAY

For analysis using GAMMA-RAY, you need to upload SNP & phenotype file.

PLINK DATA VCF DATA TRAW EMMA

Data description

--------- Genotype Data ---------
PLINK BED/BIM/FAM
PLINK format consists of three files: BED (binary genotype data), BIM (variant information), and FAM (sample information).
The three files must have the same name but different extensions.
ex) GammaSample.bed, GammaSample.bim, GammaSample.fam

[1] BED file (Binary PED)
  - Stores genotype data in binary format.
  - SNP order is defined by the BIM file, sample order is defined by the FAM file.
  - Each genotype is coded as 0, 1, 2 (number of minor alleles) or missing.

[2] BIM file
  - Contains variant information (6 columns):
    1) Chromosome
    2) SNP ID
    3) Genetic distance (Morgans)
    4) Physical position (bp)
    5) Allele 1 (minor allele)
    6) Allele 2 (major allele)

[3] FAM file
  - Contains sample information (6 columns):
    1) Family ID (FID)
    2) Individual ID (IID)
    3) Paternal ID (0 if unknown)
    4) Maternal ID (0 if unknown)
    5) Sex (1=male, 2=female, 0=unknown)
    6) Phenotype (-9 or 0=missing)

The three files must be consistent, with BED storing genotypes in SNP order from BIM and sample order from FAM.
--------- Phenotype Data ---------
A file containing multiple phenotypes (traits) for analysis, where each row corresponds to a sample and each column corresponds to a phenotype, in the same sample order as in the genotype (FAM) file.
Phenotypes can be continuous (e.g., expression levels of multiple genes, height, weight) or categorical (e.g., multiple binary disease statuses).
ex) 5 samples, 3 phenotypes:
     ID  Trait1  Trait2  Trait3
     S1  5.32  1.47  3.42
     S2  4.89  7.12  1.36
     S3  6.01  0.44  2.87
     S4  5.77  -2.19  1.11
     S5  -3.44  2.87  5.19

--------- Genotype Data ---------
VCF (Variant Call Format)
VCF format is a widely used text file format that stores variant information and sample genotype calls in a single file.
It consists of a header section with metadata lines starting with ## and a tab-delimited data section.
Each row in the data section represents a variant and contains the following columns:
    1) CHROM: Chromosome
    2) POS: Base-pair position
    3) ID: Variant identifier (e.g., rsID) or '.' if unknown
    4) REF: Reference allele
    5) ALT: Alternate allele(s)
    6) QUAL: Quality score
    7) FILTER: Filter status
    8) INFO: Additional variant information
    9) FORMAT: Genotype data format description
Following these columns, genotype calls for each sample are included.

Genotypes are typically encoded as 0 (reference allele), 1 (alternate allele), or '.' (missing).
VCF is commonly used in sequencing and genotyping projects such as the 1000 Genomes Project.

For detailed format specifications, please refer to the VCFv4.2 standard on hts-specs GitHub.
--------- Phenotype Data ---------
A file containing multiple phenotypes (traits) for analysis, where each row corresponds to a sample and each column corresponds to a phenotype, in the same sample order as in the genotype (FAM) file.
Phenotypes can be continuous (e.g., expression levels of multiple genes, height, weight) or categorical (e.g., multiple binary disease statuses).
ex) 5 samples, 3 phenotypes:
     ID  Trait1  Trait2  Trait3
     S1  5.32  1.47  3.42
     S2  4.89  7.12  1.36
     S3  6.01  0.44  2.87
     S4  5.77  -2.19  1.11
     S5  -3.44  2.87  5.19

--------- Genotype Data ---------
TRAW Format
The TRAW file is a variant-major additive component file produced --recode A-transpose option.
It is a tab-delimited text file containing one header line followed by one line per variant.

Each line contains N+6 fields (N = number of samples):
    1) CHR: Chromosome code
    2) SNP: Variant identifier (e.g., rsID)
    3) (C)M: Genetic position in Morgans or centiMorgans
    4) POS: Base-pair coordinate
    5) COUNTED: Counted allele (defaults to A1)
    6) ALT: Other allele(s), comma-separated

--------- Phenotype Data ---------
A file containing multiple phenotypes (traits) for analysis, where each row corresponds to a sample and each column corresponds to a phenotype, in the same sample order as in the genotype (FAM) file.
Phenotypes can be continuous (e.g., expression levels of multiple genes, height, weight) or categorical (e.g., multiple binary disease statuses).
ex) 5 samples, 3 phenotypes:
     ID  Trait1  Trait2  Trait3
     S1  5.32  1.47  3.42
     S2  4.89  7.12  1.36
     S3  6.01  0.44  2.87
     S4  5.77  -2.19  1.11
     S5  -3.44  2.87  5.19

--------- Genotype Data ---------
EMMA (Efficient Mixed-Model Association)
EMMA genotype data is usually a plain numeric matrix without headers or row names.
Rows represent samples and columns represent SNPs, but sample and SNP IDs are managed separately.
Each cell contains genotype calls coded as 0, 1, or 2 indicating the number of minor alleles.

Example (no headers or SNP/sample IDs):
        0 1 0 2
        1 1 2 0
        0 0 1 1

Here, each row corresponds to a sample and each column corresponds to a SNP.
'0' means homozygous major allele, '1' heterozygous, and '2' homozygous minor allele.
--------- Phenotype Data ---------
EMMA (Efficient Mixed-Model Association)
For EMMA multivariate phenotype analysis, phenotype data includes multiple traits simultaneously.
Each row corresponds to a sample and each column corresponds to a different phenotype.
Sample order must match the genotype data.

Example phenotype matrix with multiple traits:
    5.32 1.47 3.42
    4.89 7.12 1.36
    6.01 0.44 2.87
    5.77 -2.19 1.11
    -3.44 2.87 5.19

Each column represents a phenotype (trait), and rows represent samples.
This format enables EMMA to jointly analyze multiple traits, accounting for their correlations.

GAMMA-RAY

Generalized Analysis of Molecular variance for Mixed model Analysis GAMMA-RAY is a method that can simultaneously analyze many phenotypes as well as correct for population structure. (Click the bold text if you want to use the program manually.)

Upload files to use GAMMA-RAY

For analysis using GAMMA-RAY, you need to upload SNP & phenotype file.