bedtools/bedtools_bedtobam
Converts
BED
GFF
VCF
BAM
Description
Converts feature records (bed/gff/vcf) to BAM format.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input file (bed/gff/vcf). |
--genome -g | file required | Input genome file. NOTE: This is not a fasta file. This is a two-column tab-delimited file where the first column is the chromosome name and the second their sizes. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file output | Output BAM file to be written. |
Options
Name | Type & Properties | Description |
|---|---|---|
--map_quality -mapq | integer | Set the mappinq quality for the BAM records. |
--bed12 | boolean_true | The BED file is in BED12 format. The BAM CIGAR string will reflect BED "blocks". |
--uncompress_bam -ubam | boolean_true | Write uncompressed BAM output. Default writes compressed BAM. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output"
map_quality: [ 255 ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.3.1 \
-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 v0.3.1
Uses
0 relationships
No component dependencies found.