Germline Variants Samples

A relatively simple schema with the essential information for genetic germline variant samples with support for pedigree information. The assumed setting is as follows.

  • Each bio entity is a patient/person/donor.
  • Each donor gives one normal (bio) sample (e.g., blood or saliva) and each sample has at one DNA library.
  • The pedigree has to be described in a way such that all members who donated a sample are connected.
  • Within each pedigree, the flag for “affected” specifies the same genetic disease (i.e., in a polydactily family, only members affected with this phenotype are flagged as affected).


The requirement of one DNA HTS library for each donor can be dropped in the future.

Germline Fields

The following fields must be present for germline variants sample sheets.

  • BioSample
    • fatherPk – pk value of the father
    • motherPk – pk value of the mother
    • sex – sex of the patient
    • affected – “is affected” flag

Germline TSV Schema

Additionally, there is an alternative to defining schemas in JSON format for germline variants sample sheets. Instead, a TSV-based schema can be used.

Optionally, the schema can contain meta data, starting with [Metadata] INI-style section header (the data section has to start with [Data]).

schema	germline_variants
schema_version	v1
title	Example germline study
description	The [Data] section is similar to a PEDigree file


The schema and schema_version lines are optional.

If the file does not start with an INI-style section header, it starts with tab-separated column names. An example is shown below:

patientName	fatherName	motherName	sex	affected	libraryType	folderName	hpoTerms
12_345	12_346	12_347	1	2	WGS	12-345	HP:0009946,HP:0009899
12_348	12_346	12_347	1	1	WGS	12-348	.
12_346	0	0	1	1	.	.	.
12_347	0	0	2	1	WGS	12-347	.

They are as follows:

  1. patientName – name of the patient, used for identifying the patient in the sample sheet. This value will be used as the secondary id of the BioEntity of the patient.
  2. fatherName – name of the patient’s father, use 0 or . for founder. This refers to the patientName of the patient’s father.
  3. mother – name of the patient’s mother, use 0 or . for founder. This refers to the patientName of the patient’s mother.
  4. sex – flag for sex, one of M: male, F: female, .: unknown/missing, or 0, 1, 2, as in PED.
  5. affected – flag for being affected, one of Y: yes, N: no, .: unknown/missing, or 0, 1, 2, as in PED.
  6. folderName – a folder name to search the library’s FASTQ files for, . if not sequenced. The list of base folders to search for is given in the configuration and this folder is searched for a folder with the name given here. Thus, no absolute path is given here, only the folder name.
  7. hpoTerms – a comma-separated list of HPO terms to label the patient with, . if empty.
  8. libraryType – a rough classification of the library type {WGS, WES, Panel-seq}, . if not sequenced or unknown
  9. kitName/kitType – type/name of the kit used (free text/controlled vocabulary), . if not sequenced or unknown; optional. This column can be left out.
  10. kitVersion – version of the kit used, . if not sequenced or unknown; optional. This column can be left out.

Optionally, the following fields can be added:

  • seqPlatform can be one of Illumina and PacBio, default is Illumina