Multi Bam Cov

# 2) Count only proper pairs with MAPQ >= 20
multiBamCov \
  -bams sample1.bam sample2.bam sample3.bam \
  -bed exons.bed \
  -q 20 \
  -p

# 3) Count split alignments on the same strand
multiBamCov \
  -bams rna1.bam rna2.bam \
  -bed exons.bed \
  -split \
  -s

Recommended Workflow

1. Prepare the region file that defines the reporting frame, because output is one row per input interval.
2. Decide whether the counts should exclude duplicates and failed-QC reads (default) or include them (-D, -F).
3. Set -q, -p, -s / -S, and -split deliberately so all BAMs are counted under the same policy.
4. Import the appended per-BAM count columns into downstream statistical or visualization tooling.

Guardrails

• -bams and -bed are both required.
• This tool reports counts per interval per BAM, not per-base depth tracks like genomeCoverageBed.
• -D and -F widen the reads included in counting; the default excludes duplicates and failed-QC reads.
• -q defaults to 0, so low-quality alignments are included unless you raise the threshold.
• Prefer indexed, queryable BAMs for practical performance on large region sets.