Genotype format converting tool : FCgene

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Genotype format changing tool

How to Convert Format of Genotype SNP Data

fcGENE is a free, open-source Format Converting tool for genotype SNP data. Its main purpose is to simplify the process of imputation-based Genome wide association studies(GWAS). fcGENE is a <alt="genotype">genotype</alt="genotype"> <alt="format">format</alt="format"> <alt="converter">converter</alt="converter"> and can read and convert genotype SNP data having the format of the software:

PLINK, a tool for analysing genotype/phenotype data,

SNPTEST, a tool used for the analysis of single SNP association in genome-wide studies,



    and the genotype imputation tools like: MACH, IMPUTE BEAGLE, and BIMBAM.

    Functions of fcGENE can be divided into two parts. First, it uploads differently formatted genotype data to perform SNP-wise and individual-wise quality control and /or to generate the files required for different GWA analysis tools. It also generates the templates of commands required by the specified GWA tool.

    The second part of its function is to convert imputation results into different kinds of required file formats. Transformation of imputation result can be performed together filtration of SNPs based on their imputation quality. Cut-offs for different quality measures can be given as command line in fcGENE so that it can automatically filter the disqualified SNPs. Different quality measures including SNP-wise and sample-wise genotyping rates, minor allele frequency (MAF) and Hardy-Weinberg equilibrium (HWE) tests can be calculated with fcGENE. Genotype imputation has been recognized as an important statistical and technical step for GWAS. MACH, IMPUTE, BEAGLE and BIMBAM are the softwares that are used most frequently for imputation purpose. Similarly, SNPTEST takes into account of genotype imputation uncertainty when performing a test for SNP association between cases and controls. That is why this program seems to be useful for the analysis of single SNP association in GWAS.

    In summary the main idea behind the construction of fcGENE is that this program can be used first to convert PLINK formatted genotype data into the format of any one of above mentioned imputation programs and then to convert the imputed genotype data back to the PLINK format or SNPTEST format after the completion of imputation process.

    fcGENE is a genotype format converter and is designed for:

    • converting plink formatted genotype data into the format of any one of previously mentioned imputation programs

    • obtaining the templates of imputation commands which are necessary for the selected imputation tool,

    • converting back the imputed genotype data ( the files generated by imputation tool) into plink format after the completion of imputation process,

    • changing the input data of any any imputation tool into any other imputation software,

    • and preparing the files for SNPTEST software from PLINK formatted genotype and phenotype files and also from the files generated by previously mentioned imputation tool.

    Commands used to run fcGENE are inspired by PLINK. Thus just like as the PLINK commands, each command line of fcGENE contains commands separated by two dashes (--). For example, one can use
    ./fcgene - -help

    to display the information on how commands are used in fcGENE. The sequential order of using software for GWAS study can be considered as
    PLINK=>fcGENE=>Imputation tool =>fcGENE =>PLINK.

    For example if you decide to use imputation software “MaCH " (and “mimimac") to impute your genotype
    data set and the data are given in plink format, then the imputation process can be proceeded by using softwares as follows.
    PLINK =>fcGENE=>MaCH ( and minimac) =>fcGENE=>PLINK

    First, the plink formatted genotype data should be changed into “MaCH " format. The following example explains how to convert plink format files containing in the directory “example" into mach format.
    ./fcgene --map example/ --ped example/plink.ped --oformat mach --out example/mach
    Similarly if you prefer to use IMPUTE to impute your missing genotypes, then you can <alt="convert">convert</alt="convert"> your genotype data using the following command.
    ./fcgene --map example/ --ped example/plink.ped --oformat impute --out example/impute

    To download the current version of fcGENE:

    Please visit fcGENE's homepage

    Table showing the list of genotype format converting command options, files which fcGENE can take as input and change their genotype format as output.

    program input options input files output option output files
    PLINK - -ped and - -map *.ped and *.map file - oformat plink *.ped and *.map file
    - -covar covariate file
    MACH - -ped and - -map *.ped and *.dat files - -oformat mach *.ped and *.dat files
    - -mach-geno and
    - -mach-info
    *.geno and
    *.info files
    - -mach-mlgeno and
    - -mach-mlinfo
    *.mlgeno and
    *.mlinfo files
    - -mach-mlprob and
    - -mach-mlinfo
    *.mlprob and
    *.mlinfo files
    - -minimach-prob and
    - -minimach-info
    *.prob and
    IMPUTE - -gens *.gens file - - oformat impute *.gens file
    *.strand.txt file
    SNPTEST - -gens and
    - -sample
    *.gen and
    *.sample file
    - - oformat snptest *.gen file
    *.sample file
    BEAGLE - -bgl *.bgl file - - oformat beagle *.bgl file
    - -bgl *.bgl.phased file
    - -bgl-gprobs *.bgl.gprobs file
    BIMBAM - -wbg *.geno.txt file - - -oformat bimbam *.geno.txt file
    *.pheno.txt file
    *.pos.txt file
    - -wbg *.best.guess.genotype.txt
    - -wgd *.genotype.distribution.txt

    genotype format convert change SNP data format

  • Discussion

    • Nab Raj Roshyara

      Please let me know if you have any comments or bugs on the program FCgene.

      Last edit: Nab Raj Roshyara 2012-09-25
    • Meraj Ahmad

      Meraj Ahmad - 2017-03-10

      Thanks for the software. There seems to ne one issue while I convert impute2 output into binary plink format. The bp position in plink format is column three while fcgene gives the position in column four. Please rectify so that the plink output from fcgene can correctly be used for other downstream purpose. Thanks!


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