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