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bedtools BAM to BED (version 2.30.0+galaxy2)

Convert the following BAM file to BED:

What type of BED output would you like:

Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage.:

If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data.

Use alignment's edit-distance for BED score:

Use other NUMERIC BAM alignment tag as the BED score:

What it does

bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.

The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries. For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp. However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation). This is important for RNA-seq and structural variation experiments.

If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).

This tool is part of the bedtools package from the Quinlan laboratory.

Citation

If you use this tool in Galaxy, please cite:

Bjoern A. Gruening (2014), Galaxy wrapper