5.1.24. multicov¶
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.
Note
bedtools multicov depends upon index BAM files in order to count the number of overlaps in each BAM file. As such, each BAM file should be position sorted (samtool sort aln.bam aln.sort) and indexed (samtools index aln.sort.bam) with either samtools or bamtools.
5.1.24.1. Usage and option summary¶
Usage:
bedtools multicov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed <BED/GFF/VCF>
(or):
multiBamCov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed <BED/GFF/VCF>
| Option | Description |
|---|---|
| -split | Treat “split” BAM or BED12 entries as distinct BED intervals. |
| -s | Require same strandedness. That is, only report hits in B that overlap A on the _same_ strand. By default, overlaps are reported without respect to strand. |
| -S | Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand. |
| -f | Minimum overlap required as a fraction of each A. Default is 1E-9 (i.e., 1bp). |
| -r | Require that the fraction overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B. |
| -q | Minimum mapping quality (MAPQ) allowed. Default is 0. |
| -D | Include duplicate reads. Default counts non-duplicates only |
| -F | Include failed-QC reads. Default counts pass-QC reads only |
| -p | Only count proper pairs. Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. |
5.1.24.2. Default behavior.¶
By default, multicov will report the count of alignments in each input BAM file that overlap.
$ cat ivls-of-interest.bed
chr1 0 10000 ivl1
chr1 10000 20000 ivl2
chr1 20000 30000 ivl3
chr1 30000 40000 ivl4
$ bedtools multicov -bams aln1.bam aln2.bam aln3.bam -bed ivls-of-interest.bed
chr1 0 10000 ivl1 100 2234 0
chr1 10000 20000 ivl2 123 3245 1000
chr1 20000 30000 ivl3 213 2332 2034
chr1 30000 40000 ivl4 335 7654 0
The output of multicov reflects a distinct report of the overlapping alignments for each record in the -bed file. In the example above, each line of the output reflects a) the original line from the -bed file followed by b) the count of alignments that overlap the -bed interval from each input -bam file. In the example above, the output consists of 7 columns: the first four of which are the columns from the -bed file and the last 3 are the count of overlapping alignments from the 3 input -bam files. The order of the counts reflects the order of the files given on the command line.
Note
bedtools multicov will work with a single BAM as well.
$ bedtools multicov -bams aln1.bam -bed ivls-of-interest.bed
chr1 0 10000 ivl1 100
chr1 10000 20000 ivl2 123
chr1 20000 30000 ivl3 213
chr1 30000 40000 ivl4 335
