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Prioritization of whole-exome data by random-walk analysis of protein-protein interactions

PED files

A PED file ('Pedigree file') describes the family relationships of each sample along with their gender and phenotype. PED files are typically used by software that performs genetic linkage analysis. ExomeWalker requires a PED file to analyse VCF files that comprise multiple samples.

The PED file should have no header and exactly six columns. The PED file is a white-space (space or tab) delimited file.

ColumnItemExampleExplanation
1Family IDFAM001An identifier for the family.
2Sample ID859_AA unique identifier for the sample (person).
3Father's sample ID922_B The sample ID for the father of the current individual (or 0 if the father is not represented in the pedigree).
4Mother's sample ID923_B The sample ID for the mother of the current individual (or 0 if the mother is not represented in the pedigree).
5Gender21 for male, 2 for female, 0 if unknown.
6Phenotype11 for unaffected, 2 for affected, 0 if unknown.

Exome Walker performs pedigree analysis on simple pedigrees of the kind that are usually encountered in exome sequencing studies. This comprises nuclear families segregating autosomal recessive diseases with two unaffected parents and one or more affected as well as one or more unaffected children. Any autosomal dominant pedigree is accepted, as are pedigrees segregating X-chromosomal recessive disorders. For more complicated pedigrees, it is recommended to first perform traditional linkage analysis and then to filter the VCF file accordingly before submission to the Exome Walker server.

Trio analysis is becoming increasingly important in Exome sequencing studies, as it is in principle possible to identify autosomal recessive diseases with a homozygous or compound heterozygous mutation in an affected child (for recessive diseases) as well as de novo heterozygous mutations. The Exome Walker will search for heterozygous mutations found only in an affected child in this case, but it does not perform a specialized analysis of de novo mutations, which thus would need to be performed using other software.

The following shows an example PED file for a family quartet consisting of unaffected parents and an affected son as well as an unaffected daughter.

FAM01Mother0021
FAM01Father0011
FAM01SonFatherMother12
FAM01DaughterFatherMother21

Please note that the Sample IDs (column 2 of the PED File) must exactly match the Samples IDs used in the VCF file, otherwise an error will be reported.