Version Compatibility

Reference examples tested with: bedtools 2.31+, numpy 1.26+, pandas 2.2+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• Python:

  pip show <package>

  then

  help(module.function)

  to check signatures
• CLI:

  <tool> --version

  then

  <tool> --help

  to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Coverage Analysis

"Calculate sequencing coverage" → Compute per-base or per-region depth from BAM files to assess sequencing adequacy.

• CLI:

  bedtools genomecov -ibam input.bam

  ,

  samtools depth input.bam

• Python:

  pybedtools.BedTool('input.bam').genome_coverage()

  (pybedtools)

Calculate coverage and depth across genomic regions using bedtools and pybedtools.

genomecov - Genome-wide Coverage

Per-base Coverage (bedGraph)

# Generate bedGraph from BAM (per-base depth)
bedtools genomecov -ibam alignments.bam -bg > coverage.bedGraph

# Include zero-coverage regions
bedtools genomecov -ibam alignments.bam -bga > coverage_with_zeros.bedGraph

# Split by strand
bedtools genomecov -ibam alignments.bam -bg -strand + > plus_strand.bedGraph
bedtools genomecov -ibam alignments.bam -bg -strand - > minus_strand.bedGraph

# Scale by total reads (RPM normalization)
TOTAL=$(samtools view -c alignments.bam)
SCALE=$(echo "scale=10; 1000000/$TOTAL" | bc)
bedtools genomecov -ibam alignments.bam -bg -scale $SCALE > normalized.bedGraph

# Use only 5' end of reads
bedtools genomecov -ibam alignments.bam -bg -5 > five_prime.bedGraph

# Use only 3' end of reads
bedtools genomecov -ibam alignments.bam -bg -3 > three_prime.bedGraph

Coverage Histogram

# Genome-wide coverage histogram
bedtools genomecov -ibam alignments.bam > coverage_hist.txt

# Output format: chr, depth, bases_at_depth, chr_size, fraction
# genome  0       1000000  10000000  0.1
# genome  1       5000000  10000000  0.5
# ...

Coverage from BED

# Coverage from BED intervals
bedtools genomecov -i regions.bed -g genome.txt -bg > coverage.bedGraph

# BED must be sorted
bedtools sort -i regions.bed | bedtools genomecov -i stdin -g genome.txt -bg > coverage.bedGraph

Python

import pybedtools

# From BAM
bam = pybedtools.BedTool('alignments.bam')
coverage = bam.genome_coverage(bg=True)
coverage.saveas('coverage.bedGraph')

# With zeros
coverage = bam.genome_coverage(bga=True)

# Normalized
coverage = bam.genome_coverage(bg=True, scale=0.001)

# From BED
bed = pybedtools.BedTool('regions.bed')
coverage = bed.genome_coverage(bg=True, g='genome.txt')

coverage - Coverage per Feature

Basic Coverage

# Calculate how much of each region in A is covered by B
bedtools coverage -a targets.bed -b reads.bed > coverage_per_target.bed

# Output adds 4 columns: overlaps, bases_covered, region_length, fraction
# chr1  100  200  region1  5  50  100  0.5

# From BAM
bedtools coverage -a targets.bed -b alignments.bam > coverage.bed

# Count only (no coverage calculation)
bedtools coverage -a targets.bed -b reads.bed -counts > counts.bed

Coverage Options

# Mean coverage per region
bedtools coverage -a targets.bed -b alignments.bam -mean > mean_coverage.bed

# Same strand only
bedtools coverage -a targets.bed -b alignments.bam -s > same_strand.bed

# Report depth at each position (histogram)
bedtools coverage -a targets.bed -b alignments.bam -d > per_base.bed

# Require minimum overlap
bedtools coverage -a targets.bed -b reads.bed -f 0.5 > min_overlap.bed

# Split alignments (for RNA-seq)
bedtools coverage -a exons.bed -b alignments.bam -split > exon_coverage.bed

Python

import pybedtools

a = pybedtools.BedTool('targets.bed')
b = pybedtools.BedTool('alignments.bam')

# Basic coverage
result = a.coverage(b)

# Mean coverage
result = a.coverage(b, mean=True)

# Counts only
result = a.coverage(b, counts=True)

# Per-base depth
result = a.coverage(b, d=True)

result.saveas('coverage.bed')

multicov - Counts Across Multiple BAMs

# Count reads in regions across multiple samples
bedtools multicov -bams sample1.bam sample2.bam sample3.bam -bed regions.bed > counts.txt

# Require mapping quality
bedtools multicov -bams sample1.bam sample2.bam -bed regions.bed -q 30 > counts.txt

# Split alignments
bedtools multicov -bams sample1.bam sample2.bam -bed regions.bed -s -split > counts.txt

Calculate Coverage Statistics

Mean/Median Depth

import pybedtools
import pandas as pd
import numpy as np

# Load coverage BED (from bedtools coverage -d)
bed = pybedtools.BedTool('per_base_coverage.bed')
df = bed.to_dataframe()

# Calculate stats per region
stats = df.groupby(['chrom', 'start', 'end']).agg({
    'score': ['mean', 'median', 'std', 'max']
}).reset_index()

print(stats)

Coverage Distribution

Goal: Parse a genome-wide coverage histogram to calculate mean sequencing depth and visualize the depth distribution.

Approach: Run bedtools genomecov to produce a histogram, parse the genome-wide depth and fraction columns, and compute weighted mean depth from the distribution.

import pybedtools

# Get coverage histogram
bam = pybedtools.BedTool('alignments.bam')
hist = bam.genome_coverage()

# Parse histogram
depths = []
fractions = []
for line in open(hist.fn):
    fields = line.strip().split('\t')
    if fields[0] == 'genome':
        depths.append(int(fields[1]))
        fractions.append(float(fields[4]))

# Calculate metrics
import numpy as np
mean_depth = sum(d * f for d, f in zip(depths, fractions))
print(f'Mean depth: {mean_depth:.1f}x')

Common Patterns

Target Region Coverage Summary

# Get per-region coverage stats
bedtools coverage -a targets.bed -b alignments.bam | \
    awk -v OFS='\t' '{
        mean = ($NF > 0) ? $5/$6 : 0;
        print $1, $2, $3, $4, $7, mean
    }' > summary.bed

# Regions with low coverage
bedtools coverage -a targets.bed -b alignments.bam | \
    awk '$NF < 0.8' > low_coverage.bed

Normalize to CPM (Counts Per Million)

import pybedtools

bam = pybedtools.BedTool('alignments.bam')

# Get total reads
import subprocess
result = subprocess.run(['samtools', 'view', '-c', 'alignments.bam'],
                        capture_output=True, text=True)
total_reads = int(result.stdout.strip())

# Generate CPM-normalized bedGraph
scale_factor = 1000000 / total_reads
coverage = bam.genome_coverage(bg=True, scale=scale_factor)
coverage.saveas('cpm_normalized.bedGraph')

Exon Coverage for RNA-seq

# Calculate coverage across exons (handling spliced reads)
bedtools coverage -a exons.bed -b alignments.bam -split > exon_coverage.bed

# Summarize by gene
awk -v OFS='\t' '{
    gene = $4; gsub(/_exon.*/, "", gene);
    sum[gene] += $NF * ($3-$2);
    len[gene] += $3-$2;
}
END {
    for (g in sum) print g, sum[g]/len[g];
}' exon_coverage.bed > gene_coverage.txt

bedGraph Format

# bedGraph: chr, start, end, value (0-based coordinates)
chr1    0       100     0
chr1    100     200     5.5
chr1    200     300     10.2
chr1    300     400     3.1

Key Parameters

Tool	Parameter	Description
genomecov -bg	bedGraph	Output bedGraph format
genomecov -bga	bedGraph all	Include zero coverage
genomecov -scale	Normalize	Scale values by factor
coverage -mean	Mean	Report mean coverage
coverage -d	Per-base	Report per-position depth
coverage -counts	Count	Count overlaps only
multicov -q	Quality	Minimum mapping quality

Related Skills

• bigwig-tracks - Convert bedGraph to bigWig
• alignment-files/sam-bam-basics - BAM processing
• interval-arithmetic - Intersect with regions
• chip-seq/chipseq-visualization - Peak coverage analysis