This software does not work with software for low-coverage & pooling.

To download this tool, click

PEDconvert tool converts PLINK PED files into Multiple Genes File Format. There are 3 input files for this tool.

  1. PED file: PLINK PED file
  2. MAP file: PLINK MAP file
  3. SNP Info file: SNP Info file, which is discussed below

SNP Info file contains information about each SNP on each line, and there are three columns.

  1. 1st column: SNP rsID (must be the same rsID as in the MAP file)
  2. 2nd column: Gene ID (must be an integer)
  3. 3rd column: Weight of this SNP (must be between 0 and 1)
Gene ID is the ID of gene to which the SNP belongs, and Weight is between 0 and 1.

Here is a sample SNP Info file with 5 SNPs in 2 genes.
rs1 1 0.1
rs2 1 0.9
rs3 2 0.3
rs4 2 0.2
rs5 2 0.8

Currently, PEDconvert tool is compatible with Linux systems only (please let me know if you want the tool to be compatible with Windows or Mac).

To execute this tool, type
./ [prefix of ped/map file] [SNP info file] [output file]
For example, if you have test.ped,, test.snpinfo files and output file is test.output, the command should be
./ test test.snpinfo test.output

Please contact Jae Hoon Sul at jhsul at cs dot ucla dot edu if you have more questions or suggestions.