Package org.snpsift

Class SnpSiftCmdVcf2Tped

  • All Implemented Interfaces:
    org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

    public class SnpSiftCmdVcf2Tped
    extends SnpSift
    Transform a VCF to a TPED file
    Author:
    pcingola
    • Constructor Detail

      • SnpSiftCmdVcf2Tped

        public SnpSiftCmdVcf2Tped()
      • SnpSiftCmdVcf2Tped

        public SnpSiftCmdVcf2Tped​(java.lang.String[] args)
    • Method Detail

      • init

        public void init()
        Default parameters
        Overrides:
        init in class SnpSift
      • parseArgs

        public void parseArgs​(java.lang.String[] args)
        Description copied from class: SnpSift
        Parse command line arguments
        Specified by:
        parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        parseArgs in class SnpSift
      • run

        public boolean run()
        Run annotations
        Specified by:
        run in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        run in class SnpSift
      • usage

        public void usage​(java.lang.String msg)
        Show usage message
        Specified by:
        usage in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        usage in class SnpSift
        Parameters:
        msg -
      • vcf2Tped

        public void vcf2Tped​(java.lang.String vcfFile,
                             java.lang.String tfamFile,
                             java.lang.String outTfamFile,
                             java.lang.String outTpedFile)
        Convert a VCF to a TPED file
        Parameters:
        vcfFile -
        tpedFile - Important: If the variant is NOT a SNP, we create a 'fake' snp ( A -> T ). This is done in order to be able to MAP InDels into PED files and keep compatibility with downstream programs (GenAble). Yes, it's an awful hack. YOu've been warned!