Galaxy |

Intersect BAM alignments with intervals in another files (version 0.1.0)

Which alignments in this BAM file:

overlap intervals in this BED file?:

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.

Calculate coverage based on:

Minimum overlap required as a fraction of the BAM alignment:

Alignments are only retained if the overlap with the an interval in the BED file comprises at least this fraction of the BAM alignment's length. For example, to require that the overlap affects 50% of the BAM alignment, use 0.50

Require reciprocal overlap.:

If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval.

Report only those alignments that **do not** overlap the BED file.:

What it does

This tool creates a new BAM alignment file based on alignments that overlap (or optionally, those that do not overlap) intervals in another BED file. Example usage would be to cull a BAM file from an exome capture experiment to include on the "on-target" alignments.

Note that each BAM alignment is treated individually. Therefore, if one end of a paired-end alignment overlaps an interval in the BED file, yet the other end does not, the output file will only include the overlapping end.

Note that a BAM alignment will be sent to the output file once even if it overlaps more than one interval in the BED file.

This tool requires that bedtools has been installed on your system.

This tool is part of the bedtools package from the Quinlan laboratory. If you use this tool, please cite Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.