.. _multicov: ############### *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. ========================================================================== Usage and option summary ========================================================================== **Usage**: :: bedtools multicov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed **(or)**: :: multiBamCov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed ============ ================================================================ 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 -bed record. Default is 1E-9 (i.e., 1bp). **-r** Require that the fraction overlap is reciprocal for -bed and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap 90% of the -bed record and the -bed record _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. ============ ================================================================ ========================================================================== Default behavior. ========================================================================== By default, ``multicov`` will report the count of alignments in each input BAM file that overlap. .. code-block:: bash $ 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. .. code-block:: bash $ 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