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fcGENE

Description

fcgene website

This is a format conversion tool for genotype data such as PLINK and MACH. The usage is two-fold. First, convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM. Second, transform imputed data into different file formats like PLINK, HAPLOVIEW, EIGENSOFT and SNPTEST. Readable file formats: plink-pedigree (ped and map), plink-raw, plink-dosage, mach , minimac, impute, snptest, beagle and bimbam. Similarly all kinds of imputation of outputs are also accepted. Formats which can be generated by fcGENE: plink-pedigree, plink-raw, plink-dosage, mach-inputs, minimac-inputs, impute-inputs, beagle-inputs and bimbam-inputs, HAPLOVIEW-inputs, EIGENSOFT-inputs.

Environment Modules

Run module spider fcgene to find out what environment modules are available for this application.

Environment Variables

  • HPC_FCGENE_DIR - installation directory
  • HPC_FCGENE_BIN - executable directory

Categories

biology, genomics, variant_calling