Dear resrarchers who work in GWAS
I have two PLINK file formats of map and pad. My question is, can both file formats use in GAPIT software? If not, how to change both file formats to suitable format for GAPIT. Thanks...
Widya Pintaka Bayu Putra GAPIT (Genome Association and Prediction Integrated Tool) is a software suite for analyzing and predicting genome-wide associations in plants. GAPIT requires two types of input files to function: a genotype file and a phenotypic file.
The genotype file should be in PLINK format and contain information about your samples' genotypes at each genetic marker. The file should have the extensions.bed,.bim, and.fam. The genotyping data is contained in the.bed file, the marker information is contained in the.bim file, and the sample information is contained in the.fam file.
The phenotypic file should be a tab-delimited text file containing columns for sample IDs, trait values, and any other pertinent data, such as covariates.
Regarding your query, it is conceivable that both file types are incompatible with GAPIT. You will need to convert both files to the GAPIT-compatible format. For further information on how to prepare your input files, consult the GAPIT handbook.
If you have a map and a pad file, you must convert these to the PLINK format (bed, bim, fam) with the necessary program or script. To convert the files to PLINK format, use the 'plink' command line utility.
Thanks for the information. Can you help me to change my map and pad formats to compatible format for GAPIT? Thanks...
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