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.
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. |
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`. |
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. |
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 Relationships
Used by
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Current component
tabix/tabix_indexbiobox v0.5.0
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