tabix/tabix_index

index

tabix

htslib

vcf

bed

gff

Description

Build a tabix (.tbi) or CSI (.csi) index for a BGZF block-compressed,
position-sorted file (VCF, BED, GFF, SAM, GAF) so it can later be queried by
region. BAM/CRAM/BCF inputs are also supported, producing .bai/.crai/.csi
indexes as appropriate.

Type

bash_script

License

MIT/Expat

Keywords

index

tabix

htslib

vcf

bed

gff

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

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

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

Inputs

Name	Type & Properties	Description
--input	file required	BGZF block-compressed, position-sorted file to index. Typically a `.vcf.gz`, `.bed.gz`, `.gff.gz`, `.sam.gz`, or `.gaf.gz` file, but `.bam`, `.cram`, and `.bcf` files are also supported.

Name

Type & Properties

--input

file

required

Outputs

Name	Type & Properties	Description
--output_index	file required output	Resulting index file. The file type depends on the input file type and whether `--csi` was set. Typically a `.tbi` but can also be `.csi`, `.bai`, or `.crai`.

Name

Type & Properties

--output_index

file

required

output

Options

Name	Type & Properties	Description
--preset -p	string	Format preset to use for the sequence/begin/end/comment/skip-lines settings. Suppresses `--sequence`. If none of `--preset`, `--sequence`, `--begin`, `--end`, `--comment`, `--skip_lines`, or `--zero_based` is set, tabix attempts to detect the format from the `--input` file extension, falling back to GFF-preset settings (`--sequence 1 --begin 4 --end 5 --comment '#' --skip_lines 0`) if detection fails.
--sequence -s	integer	Column number for sequence (chromosome/contig) names. Ignored when `--preset` is set.
--begin -b	integer	Column number for region start.
--end -e	integer	Column number for region end. If the format has no end column, set this to the same value as `--begin`.
--skip_lines -S	integer	Skip the first `N` lines of the input file.
--comment -c	string	Skip lines starting with this character.
--zero_based	boolean_true	Coordinates in the input file are zero-based, half-open.
--force -f	boolean_true	Overwrite an existing index without asking.
--csi -C	boolean_true	Generate a CSI index instead of the default TBI. Required for chromosomes larger than 2^29 bases.
--min_shift -m	integer	Set the minimal interval size for CSI indices to `2^INT`. Default: 14.

Name

Type & Properties

--preset

-p

string

--sequence

-s

integer

--begin

-b

integer

--end

-e

integer

--skip_lines

-S

integer

--comment

-c

string

--zero_based

boolean_true

--force

-f

boolean_true

--csi

-C

boolean_true

--min_shift

-m

integer