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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.

Choose data collections or provide your own file URLs: Select the phase of the 1000 Genomes project for which you wish to perform a VCF to PED conversion. 

Select Phase 3 / Phase 1 populations: If you have selected either 'Phase 3' or 'Phase 1' from the 'Choose data collections or provide your own file URLs' section (above), you are now able to select the populations of the 1000 Genomes project for which you wish to perform a VCF to PED conversion. You are able to select one, or more, of the individual populations from the 1000 Genomes Project, to produce PED files for particular populations of interest.

If you have selected 'Provide file URLs' from the 'Choose data collections or provide your own file URLs' section (above), you are now able to define URLs that contain files that contain the variation and frequency data you want the VCF to PED Converter to use.

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).

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