Pedigree / PED files

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited September 2017 in Dictionary

A pedigree is a structured description of the familial relationships between samples.

Some GATK tools are capable of incorporating pedigree information in the analysis they perform if provided in the form of a PED file through the --pedigree (or -ped) argument.


PED file format

PED files are tabular text files describing meta-data about the samples. See http://www.broadinstitute.org/mpg/tagger/faq.html and http://zzz.bwh.harvard.edu/plink/data.shtml#ped for more information.

The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory:

  • Family ID
  • Individual ID
  • Paternal ID
  • Maternal ID
  • Sex (1=male; 2=female; other=unknown)
  • Phenotype

The IDs are alphanumeric: the combination of family and individual ID should uniquely identify a person. If an individual's sex is unknown, then any character other than 1 or 2 can be used in the fifth column.

A PED file must have 1 and only 1 phenotype in the sixth column. The phenotype can be either a quantitative trait or an "affected status" column: GATK will automatically detect which type (i.e. based on whether a value other than 0, 1, 2 or the missing genotype code is observed).

Affected status should be coded as follows:

  • -9 missing
  • 0 missing
  • 1 unaffected
  • 2 affected

If any value outside of -9,0,1,2 is detected, then the samples are assumed to have phenotype values, interpreted as string phenotype values.

Note that genotypes (column 7 onwards) cannot be specified to the GATK.

You can add a comment to a PED or MAP file by starting the line with a # character. The rest of that line will be ignored, so make sure none of the IDs start with this character.

Each -ped argument can be tagged with NO_FAMILY_ID, NO_PARENTS, NO_SEX, NO_PHENOTYPE to tell the GATK PED parser that the corresponding fields are missing from the ped file.

Example

Here are two individuals (one row = one person):

FAM001  1  0 0  1  2
FAM001  2  0 0  1  2
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