SnpSift Vcf2Tped

Convert from VCF to PLINK's TPED file format.

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

Usage

java -jar SnpSift.jar vcf2tped [options] file.tfam file.vcf outputName

Option	Description	Default
-f	Force. Overwrite new files if they exist	false
-num	Use only numbers {1, 2, 3, 4} instead of bases	false
-onlySnp	Use only SNPs when converting VCF to TPED	false
-onlyBiAllelic	Use only bi-allelic variants	false
-useMissing	Use entries with missing genotypes (otherwise they are filtered out)	true
-useMissingRef	Use entries with missing genotypes marking them as 'reference' instead of 'missing'	false

Parameter	Description
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

Features

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 to "fake" SNPs (some programs have problems handling non-SNP variants).
    • -onlySnp option filters out non SNP variants.
  • Missing variants:
    • By default, entries with missing genotypes are included and marked as missing in the TPED file.
    • -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