gatk4/gatk4_createsequencedictionary

reference

indexing

GATK

GATK4

sequence dictionary

Description

Creates a sequence dictionary (.dict file) for a reference sequence.

This tool builds a sequence dictionary file from a reference sequence
provided in FASTA format. The output file contains a header but no
records and the header contains only sequence records. A sequence
dictionary is required by many GATK tools (such as HaplotypeCaller)
that process the reference genome.

Type

bash_script

License

Apache-2.0

Keywords

reference

indexing

GATK

GATK4

sequence dictionary

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.dict"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/gatk4/gatk4_createsequencedictionary/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input -R	file required	Input reference FASTA file (optionally gzipped).

Name

Type & Properties

--input

-R

file

required

Output

Name	Type & Properties	Description
--output -O	file required output	Output `.dict` file containing only the sequence dictionary.

Name

Type & Properties

--output

-O

file

required

output

Options

Name	Type & Properties	Description
--alt_names -AN	file	Optional file containing alternative names for the contigs. Tools may use this information to consider different contig notations as identical (e.g. `chr1` and `1`). The alternative names will be put into the appropriate `@AN` annotation for each contig. No header. The first column is the original name, the second column is an alternative name. One contig may have more than one alternative name.
--genome_assembly -AS	string	Genome assembly identifier (e.g. `GRCh38`) to put into the `AS` field of each sequence dictionary entry.
--num_sequences	integer	Stop after writing this many sequences. For testing.
--species -SP	string	Species name to put into the `SP` field of each sequence dictionary entry.
--truncate_names_at_whitespace	boolean	Make the sequence name the first word from the `>` line in the FASTA file. By default the entire contents of the `>` line is used, excluding leading and trailing whitespace. Default: true.
--uri -UR	string	URI to put in the `UR` field of the sequence dictionary entries, describing where the reference file can be found. If not supplied, the absolute path of the input reference file is used.

Name

Type & Properties

--alt_names

-AN

file

--genome_assembly

-AS

string

--num_sequences

integer

--species

-SP

string

--truncate_names_at_whitespace

boolean

--uri

-UR

string