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Build GATK4 Genome Dictionary Specifications

Process Details

  • Name: build_gatk4_genome_dictionary
  • Process UUID: hpzri68dlwv1d4cv294bqckkduptc0
  • Process Group: gatk4

Overview

This process creates a sequence dictionary for a reference genome sequence, which is an essential prerequisite for many downstream genomic analysis workflows. The sequence dictionary file contains metadata about the reference sequences including sequence names, lengths, and other properties required by GATK and other bioinformatics tools for proper chromosome/contig identification and validation.

This process is implemented in Bash, utilizing GATK's CreateSequenceDictionary tool along with samtools for FASTA indexing.

Key Functionality

  • Sequence Dictionary Creation: Generates a .dict file containing sequence metadata from a FASTA reference genome
  • FASTA Indexing: Creates a .fai index file using samtools for efficient sequence access
  • Reference Preparation: Prepares reference genome files in the format required by GATK4 tools and workflows

Input/Output Specification

Inputs

Required Inputs

  • Reference Genome
    • Description: Reference genome sequence in FASTA format
    • Format: FASTA (.fasta, .fa, .fas)

Outputs

  • Genome Dictionary
    • Description: Sequence dictionary file containing metadata for each sequence in the reference genome, including sequence names, lengths, and checksums
    • Format: Dictionary (.dict)

Parameters & Settings

This process does not have user-configurable parameters.

References & Resources

  • Tool Documentation: GATK CreateSequenceDictionary - https://gatk.broadinstitute.org/hc/en-us/articles/360037068312-CreateSequenceDictionary-Picard
  • Related Papers: McKenna A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-303. doi:10.1101/gr.107524.110