SnpSift Vcf2Tped - SnpEff & SnpSift
Author: Pablo Cingolani
Description: SnpEff and SnpSift

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# SnpSift Vcf2Tped

Convert from VCF to PLINK's TPED file format.

The `vcf2tped` command uses a VCF and a TFAP file as input, creating a TPED and a consolidated TFAM as outputs.

Command line options are:

    $ java -jar SnpSift.jar vcf2tped
    SnpSift version 1.9d (build 2013-04-26), by Pablo Cingolani
    Usage: java -jar SnpSift.jar vcf2tped [options] file.tfam file.vcf outputName
    Options:
            -f             : Force. Overwrite new files if they exist. Default: false
            -onlySnp       : Use only SNPs when converting VCF to TPED. Default: false
            -onlyBiAllelic : Use only bi-allelic variants. Default: false
            -useMissing    : Use entries with missing genotypes (otherwise they are filtered out). Default: false
            -useMissingRef : Use entries with missing genotypes marking them as 'reference' instead of 'missing'. Default: false
    Parameters:
            file.tfam      : File with genotypes and groups information (in PLINK's TFAM format)
            file.vcf       : A VCF file (variants and genotype data)
            outputName     : Base name for the new TPED and TFAM files.

`vcf2tped` command supports the following features:

- Output a TPED file:
  - Only samples present in both the input TFAM and the input VCF files are in the output TPED.
  - Bi-allelic filter: `-onlyBiAllelic` option filters out non bi-allelic variants.
  - Non SNP variants (InDels, MNPs, etc):
    - InDels and other non-SNP variants are converted for "fake" SNPs (some programs have problems handling non-SNP variants).
    - `-onlySnp` option filters out non SNP variants.
  - Missing variants:
    - Variants having missing data are filtered out by default.
    - `-useMissing` uses missing variants in TPED file.
    - `-useMissingRef` Converts missing variants to reference genotype.
- Output TFAM file:
  - Only samples present in both the input TFAM and the input VCF files are in the output TFAM.
  - Samples are re-ordered to have the same order as the VCF file