VCF to PED Converter
The VCF to PED converter allows users to parse a vcf file (specification) to create a linkage pedigree file (ped) and a marker information file, which together may be loaded into ld visualization tools like Haploview. There is both an online version of this tool and a perl script
The documentation for the online version can be found by clicking on the icon at the top of VCF to PED converter.
A perl API script version of the converter tool is available from the ftp site.
This script converts locally or remotely accessible vcf files to linkage pedigree files. If the input file is only remotely accessible then it must be compressed by bgzip and indexed by tabix. There is no requirement to compress vcf files if they are held locally, but large files will be read more quickly using tabix. If the vcf file is compressed then you must have tabix installed.
The script is run from the command line and it takes the following arguments:
Here is an example of a command line for running the script:
perl vcf_to_ped_converter.pl -vcf https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr13.phase1_integrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz -sample_panel_file https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.sample_panel -region 13:32889611-32973805 -population GBR -population FIN