bedtools/bedtools_bedtobam
Converts
BED
GFF
VCF
BAM
Description
Converts feature records to BAM format.
Converts genomic intervals from BED, GFF, or VCF formats into BAM format,
creating aligned sequence records that can be used with standard BAM tools.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input genomic intervals file in BED, GFF, or VCF format. **Requirements:** - BED files must be at least BED4 format (requires name field) - File must contain valid genomic coordinates |
--genome -g | file required | Genome file defining chromosome names and sizes. **Format:** Two-column tab-delimited file: ``` chr1 249250621 chr2 243199373 ``` **Note:** This is NOT a FASTA file. Use `samtools faidx` to create from FASTA if needed. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Output BAM file containing converted genomic intervals. **Format:** Standard BAM format (compressed by default) |
Options
Name | Type & Properties | Description |
|---|---|---|
--map_quality -mapq | integer | Set the mapping quality for the BAM records. **Range:** 0-255 (higher values indicate better quality) **Default:** 255 (maximum quality) |
--bed12 | boolean_true | Process BED file as BED12 format with blocked intervals. **Features:** - BAM CIGAR string reflects BED blocks (exons/introns) - Useful for representing spliced alignments - Requires BED12 format input |
--uncompress_bam -ubam | boolean_true | Write uncompressed BAM output. **Default behavior:** Writes compressed BAM **Use case:** When downstream tools require uncompressed format |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.bam"
map_quality: [ 255 ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.4.1 \
-main-script target/nextflow/bedtools/bedtools_bedtobam/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
bedtools/bedtools_bedtobambiobox v0.4.1
Uses
0 relationships
No component dependencies found.