Convert from VCF to PLINK's TPED file format.
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:
-onlyBiAllelicoption 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).
-onlySnpoption filters out non SNP variants.
- Missing variants:
- Variants having missing data are filtered out by default.
-useMissinguses missing variants in TPED file.
-useMissingRefConverts 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