FcGENE

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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.

Required Modules

Serial

  • fcgene

System Variables

  • HPC_FCGENE_DIR





Validation

  • Validated 4/5/2018