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fcGENE: Genotype format converter

Posted on by Robin Ding Leave a comment Bio-Informatics, Medical Science Apps., Statistics
5.0

Main application is twofold: first to convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM, second to 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.
Further application:
-obtaining templates of necessary imputation commands and commands of other imputation tool
– Quality control according as MAF,HWE & CALLRATE.

key words: genotype transformation, convert genotype format, imputation output, PLINK, IMPUTE, MACH, minimac, HAPLOVIEW, BEAGLE, BIMBAM,EIGENSOFT.

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Website http://www.imise.uni-leipzig.de/en/Groups/GenStat/Tools/index.jsp
Tags
Platform Linux Windows
Features
  • can make SNP-wise and Individual-wise Quality Control and can filter disqualified SNPs and individuals while transoforming data
  • can perform two-way format conversion of genotype SNP Data (e.g. PLINK -> imputation tool and imputation tools -> PLINK) . It can read and write both plink-formatted pedigree and binary files
  • can filter impued SNPs on the basis of imputation quality score
  • can generate templates of commands GWA analysis tools
  • converts the genotype data from the format of one imputation tool to other.
  • Transformation of imputation references into plink-format. This helps to compare genotype data with the reference panel.
  • can creates of snp data in GenABEL format from the data originally given in different other formats
  • can generate differently formatted files containing expeceted dose of minor allele frequency
  • very helpful for researchers working on the area of statistical genetics.
  • written in c++, use of STL containers
  • can read and write gezipped files
  • can calculate FST with --fst command
  • can read and write standard genotype data with counts of alleles and allele doses
  • can create vcf-format files used for BEAGLE4