VCF to PED Converter

The VCF to PED Converter tool converts VCF file to create a linkage pedigree file (PED) and a marker information file, which may be loaded into other variation data analysis tools, such as PLINK and Haploview. You can choose to convert a VCF file of data taken from the 1000 Genomes project, or you can supply the VCF to PED Converter tool with your own files.

When you reach the VCF to PED Converter web interface, you will be presented with a form to define the allele frequency data to want to retreive.

Name for this job (optional): naming each of your data requests with a unique name allows you to track and search the list of your submitted jobs.

Species: The VCF to PED Converter tool is based on population frequency data generated by the 1000 Genomes project, and is therefore only available for the human GRCh37 assembly, which is selected by default.

Region Lookup: Define your genomic region of interest in the format chromosome#:Start_coordinate-End_coordinate e.g 4:122868000-122946000.

Genotype file URL: Define a URL that contains a VCF file that contains the population genotypes.

Sample-population mapping file URL: Define a URL that contains a file which lists all the individuals and the populations from which they come.

Base format: Choose how to express the genotypes. You can either select 'Bases' (i.e ATGC) or 'Numbers' (i.e 1234).

Biallelic: Exclude sites with more than two alleles from output.

Output: The output of the VCF to PED Converter is a PED file and a Marker Information file, which can be individually downloaded and used in downstream applications.