bedtools/bedtools_bamtobed
Converts
BAM
BED
BED6
BEDPE
Description
Converts BAM alignments to BED6 or BEDPE format.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input BAM file. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Output BED file. |
Options
Name | Type & Properties | Description |
|---|---|---|
--bedpe | boolean_true | Write BEDPE format. Requires BAM to be grouped or sorted by query. |
--mate1 | boolean_true | When writing BEDPE (-bedpe) format, always report mate one as the first BEDPE "block". |
--bed12 | boolean_true | Write "blocked" BED format (aka "BED12"). Forces -split. See http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1 |
--split | boolean_true | Report "split" BAM alignments as separate BED entries. Splits only on N CIGAR operations. |
--splitD | boolean_true | Split alignments based on N and D CIGAR operators. Forces -split. |
--edit_distance -ed | boolean_true | Use BAM edit distance (NM tag) for BED score. - Default for BED is to use mapping quality. - Default for BEDPE is to use the minimum of the two mapping qualities for the pair. - When -ed is used with -bedpe, the total edit distance from the two mates is reported. |
--tag | string | Use other NUMERIC BAM alignment tag for BED score. Default for BED is to use mapping quality. Disallowed with BEDPE output. |
--color | string | An R,G,B string for the color used with BED12 format. Default is (255,0,0). |
--cigar | boolean_true | Add the CIGAR string to the BED entry as a 7th column. |
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 v0.3.0 \
-main-script target/nextflow/bedtools/bedtools_bamtobed/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
bedtools/bedtools_bamtobedbiobox v0.3.0
Uses
0 relationships
No component dependencies found.