🏷️ Naming Conventions

Scope and Tool Compatibility¶

This document defines naming conventions required to run analyses in cohort mode with legacy tools:

GATK 3.5
MTOOLBox

Legacy tools only

The directory and subdirectory naming conventions described in this document are mandatory for GATK 3.5 and MTOOLBox. They are not required for GATK ≥ 4.6.

With GATK 4.6, sample directory names are ignored by the pipeline and may be any arbitrary string (e.g. NEUMA640ZBR).

Directory Naming¶

Format¶

[ProjectCode]_[SampleType]

ProjectCode
Exactly 7 characters: [a-zA-Z0-9]
Example: CN99999
SampleType
One of:
- exome
- wgs

Examples¶

CN99999_exome
CN99999_wgs

Subdirectory Naming¶

Format¶

[ProjectCode][SampleID][Role]_[SampleTypeShort]

ProjectCode — 7 characters ([a-zA-Z0-9])
SampleID — 2 characters (e.g. 01)
Role — 1 character (P, F, M)
SampleTypeShort — must be ex

Example¶

CN9999901F_ex

FASTQ Naming Convention¶

This FASTQ naming convention applies to all tools, including GATK 3.5 and GATK 4.6.

It is based on the Illumina specification: support.illumina.com/help/BaseSpace_Sequence_Hub_OLH_009008_2/Source/Informatics/BS/NamingConvention_FASTQ-files-swBS.htm

Sequencing-type suffix¶

_ex — exome sequencing
_wg — whole genome sequencing

Example¶

CN9999901P_ex_S5_L001_R1_001.fastq.gz

Expected Directory Layout¶

Required for cohort mode (legacy)

This directory layout is required when running GATK 3.5 or MTOOLBox in cohort mode.

CN99999_exome/
└── CN9999901P_ex/
    ├── CN9999901P_ex_S1_L001_R1_001.fastq.gz
    └── CN9999901P_ex_S1_L001_R2_001.fastq.gz