bedtools/bedtools_getfasta

sequencing

fasta

BED

GFF

VCF

sequence extraction

Description

Extract DNA sequences from a FASTA file based on feature coordinates.

Given intervals specified in BED/GFF/VCF format and a FASTA file, this tool
extracts the corresponding sequences from the FASTA file. Various output formats
are supported including FASTA (default), tab-delimited, and BED format with sequences.

Type

bash_script

License

GPL-2.0

Keywords

sequencing

fasta

BED

GFF

VCF

sequence extraction

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"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/bedtools/bedtools_getfasta/main.nf \  
  -params-file params.yaml

Input arguments

Name	Type & Properties	Description
--input_fasta -fi	file required	Input FASTA file containing sequences for extraction. The headers in the input FASTA file must exactly match the chromosome column in the BED file.
--input_bed -bed	file required	BED/GFF/VCF file containing intervals to extract from the FASTA file. BED files containing a single region require a newline character at the end of the line, otherwise a blank output file is produced.
--rna	boolean_true	The FASTA is RNA not DNA. Reverse complementation handled accordingly.

Name

Type & Properties

--input_fasta

-fi

file

required

--input_bed

-bed

file

required

--rna

boolean_true

Processing options

Name	Type & Properties	Description
--strandedness -s	boolean_true	Force strandedness. If the feature occupies the antisense strand, the output sequence will be reverse complemented. By default strandedness is not taken into account.
--split	boolean_true	When input is in BED12 format, create a separate FASTA entry for each block in a BED12 record. Blocks are described in the 11th and 12th columns of the BED format.
--full_header -fullHeader	boolean_true	Use full FASTA header. By default, only the word before the first space or tab is used.

Name

Type & Properties

--strandedness

-s

boolean_true

--split

boolean_true

--full_header

-fullHeader

boolean_true

Output arguments

Name	Type & Properties	Description
--output -o -fo	file required output	Output file where the extracted sequences will be written. By default, output is in FASTA format unless --tab or --bed_out is specified.
--name	boolean_true	Set the FASTA header for each extracted sequence to be the "name" and coordinate columns from the BED feature (format: name::chr:start-end).
--name_only -nameOnly	boolean_true	Set the FASTA header for each extracted sequence to be only the "name" column from the BED feature.
--tab	boolean_true	Report extracted sequences in a tab-delimited format instead of FASTA format. Output format: name<tab>sequence.
--bed_out -bedOut	boolean_true	Report extracted sequences in a tab-delimited BED format instead of FASTA format. Output format: chr<tab>start<tab>end<tab>name<tab>sequence.

Name

Type & Properties

--output

-o

-fo

file

required

output

--name

boolean_true

--name_only

-nameOnly

boolean_true

--tab

boolean_true

--bed_out

-bedOut

boolean_true