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.
Input
Name | Type & Properties | Description |
|---|---|---|
--input -R | file required | Input reference FASTA file (optionally gzipped). |
Output
Name | Type & Properties | Description |
|---|---|---|
--output -O | file required output | Output `.dict` file containing only the sequence dictionary. |
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. |
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 Relationships
Used by
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No components use this component.
Current component
gatk4/gatk4_createsequencedictionarybiobox v0.5.0
Uses
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