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bedtools MultiCovBed (version 2.30.0)

Sorted BED/bedGraph/GFF/VCF/EncodePeak file:

BAM file:

Calculation based on strandedness?:

Minimum overlap required as a fraction of A:

Default is 1E-9, i.e. 1bp.

Require that the fraction of overlap be reciprocal for A and B:

In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.

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.

Minimum mapping quality (MAPQ) allowed:

Include duplicate reads:

Default counts non-duplicates only

Include failed-QC reads:

Default counts pass-QC reads only

Only count proper pairs:

Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field

What it does

bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file.

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