Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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.


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

FAM001  1  0 0  1  2
FAM001  2  0 0  1  2
Post edited by Sheila on


Sign In or Register to comment.