File Conversion

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WISARD provides several options for file conversion and their combination provides input file formats for several software.

Available options

• --makeraw : recode genotypes as 0(major homo), 1(hetero) and 2(minor homo).
• --outphenoonly : delete columns for FID, IID, paternal ID, maternal ID and SEX.
• --outnoheader : delete headers.
• --out1case : recode case and control status as 1 and 0, respectively.

File Conversion [top]

WISARD can generate the file with the following formats:

BOOST

proposed by Wan et al. Am J Hum Genet 2010 and it provides relatively fast way to investigate GWAS level gene-gene interaction.

Convert 'sample.bed' into an input of BOOST

C:\Users\WISARD> wisard --bed sample.bed --makeraw --outphenoonly --out1case --outnoheader --out inp_boost

Running the above code generates [prefix].raw file and it can be directly used as an input for BOOST. with below constraints.

NOTE!

Since BOOST requires case/control dataset, this conversion process will not work for the dataset with continuous phenotype

Beagle

Imputation and genetic analyseis software, was proposed by (Browning et al. Am J Hum Genet 2006) and is used for imputation of missing and untyped genotypes.

Convert 'sample.bed' into an input of Beagle

C:\Users\WISARD> wisard --bed sample.bed --makebeagle --out inp_beagle

MERLIN

One of pedigree analysis package, was proposed by Abecasis et al.(2002) and it is used for family-based analysis such as haplotyping, linkage analysis, etc.

Convert 'sample.bed' into an input of MERLIN

C:\Users\WISARD> wisard --bed sample.bed --makemerlin --outmispheno X --out inp_merlin

NOTE!

Since MERLIN uses X for the notation of missing phenotype, --outmispheno X should be added!

GCTA

One of well-known toolset for an analysis of genetic dataset, was proposed Yang et al.(2011). WISARD provides computed sample relatedness matrix in the form supported from GCTA, called Genetic Relationship Matrix (GRM). In addition, generated GRM from GCTA also can be used in WISARD using --cor option.

One of the toolsets like WISARD, GCTA, also provides a comprehensive function for the association test of related genetic dataset. It is capable to compute the relationship across samples based on the genotypes named genetic relationship matrix (GRM), and the resutled GRM is coded in a binarized form. WISARD accepts this GRM format and utilizes it to subsequent analyses with --cor option. Note that the last extension of GRM outputs should be omitted when provides it as an input of WISARD.

Produce a GRM matrix using GCTA

C:\Users\WISARD> gcta64 --bfile test --autosome --make-grm --out test

Above code will produce three files: test.grm.id, test.grm.N.bin and test.grm.bin, to utilize the GRM matrix from WISARD, a command like below is required, without their last extensions (.id , .N.bin and .bin).

Utilize produced GRM matrix to QLS test from WISARD

C:\Users\WISARD> WISARD --bed test.bed --qls --cor test.grm

Multifactor Dimensionality Reduction (MDR)

The first program implmenting MDR method, written in Java. WISARD can convert input dataset applicable to MDR program, with --makemdr option.

NOTE!

Only genotype data with binary phenotype can be converted with --makemdr option!

NOTE!

Only first phenotype will be used to generate the dataset if there are multiple phenotypes were assigned!

NOTE!

With --makemdr, coding for binary phenotype will be fixed to 1=case and 0=control

Convert input dataset applicable to MDR program

C:\Users\WISARD> wisard --bed sample.bed --makemdr --out inp_mdr

IMPUTE2 and SNPTEST

Both softwares use the same input file format. IMPUTE2 was proposed by Howie et al.(2009) and is used for imputation of missing and untyped genotypes SNPTEST was proposed by Marchini et al.(2009) and is used for genome-wide association studies.

Convert 'sample.bed' into a binarized input of IMPUTE2/SNPTEST

C:\Users\WISARD> wisard --bed sample.bed --makebgen --out inp_merlin

In addition, to default binarization, its genotype data can be unzipped with gzip algorithm as follows:

Convert 'sample.bed' into a binarized input with zipped data of IMPUTE2/SNPTEST

C:\Users\WISARD> wisard --bed sample.bed --makebgen --zipbgen --out inp_merlin

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