Version Compatibility

Reference examples tested with: bcftools 1.19+, bedtools 2.31+, pandas 2.2+

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.

BED File Basics

"Work with BED files" → Read, create, and manipulate genomic interval files in BED format (0-based, half-open coordinates).

• Python: pybedtools.BedTool('file.bed') (pybedtools)
• CLI: bedtools commands

BED (Browser Extensible Data) format stores genomic intervals. Uses 0-based, half-open coordinates.

BED Format Columns

BED3:  chr  start  end
BED4:  chr  start  end  name
BED5:  chr  start  end  name  score
BED6:  chr  start  end  name  score  strand
BED12: chr  start  end  name  score  strand  thickStart  thickEnd  rgb  blockCount  blockSizes  blockStarts

Coordinate System

BED uses 0-based, half-open coordinates:

• Start: 0-based (first base is 0)
• End: exclusive (not included)
• Position 100-200 means bases at positions 100-199

Create BED Files

From Text (CLI)

# Create simple BED3
echo -e "chr1\t100\t200\nchr1\t300\t400" > regions.bed

# Create BED6 with name and strand
echo -e "chr1\t100\t200\tpeak1\t100\t+" > peaks.bed

From Python

import pybedtools

# From string
bed_string = '''chr1\t100\t200\tpeak1\t100\t+
chr1\t300\t400\tpeak2\t200\t-'''
bed = pybedtools.BedTool(bed_string, from_string=True)

# From list of tuples
intervals = [
    ('chr1', 100, 200, 'peak1', 100, '+'),
    ('chr1', 300, 400, 'peak2', 200, '-'),
]
bed = pybedtools.BedTool(intervals)

# From pandas DataFrame
import pandas as pd
df = pd.DataFrame({
    'chrom': ['chr1', 'chr1'],
    'start': [100, 300],
    'end': [200, 400],
    'name': ['peak1', 'peak2'],
    'score': [100, 200],
    'strand': ['+', '-']
})
bed = pybedtools.BedTool.from_dataframe(df)

# Save to file
bed.saveas('output.bed')

Sort BED Files

CLI

# Sort by chromosome and position
sort -k1,1 -k2,2n input.bed > sorted.bed

# Using bedtools
bedtools sort -i input.bed > sorted.bed

# Sort by chromosome, start, then end
sort -k1,1 -k2,2n -k3,3n input.bed > sorted.bed

Python

import pybedtools

bed = pybedtools.BedTool('input.bed')
sorted_bed = bed.sort()
sorted_bed.saveas('sorted.bed')

Validate BED Files

Check Format

# Check column count
awk -F'\t' '{print NF}' input.bed | sort -u

# Check for invalid coordinates (start >= end)
awk '$2 >= $3' input.bed

# Check for negative coordinates
awk '$2 < 0 || $3 < 0' input.bed

# Validate with bedtools
bedtools sort -i input.bed > /dev/null 2>&1 && echo "Valid" || echo "Invalid"

Python Validation

Goal: Programmatically validate a BED file for common format errors before using it in downstream tools.

Approach: Load the file with pybedtools, iterate through all intervals checking for negative coordinates and invalid ranges (start >= end), and return a pass/fail status with error description.

import pybedtools

def validate_bed(filepath):
    try:
        bed = pybedtools.BedTool(filepath)
        for interval in bed:
            if interval.start < 0 or interval.end < 0:
                return False, 'Negative coordinates'
            if interval.start >= interval.end:
                return False, f'Invalid interval: {interval.start} >= {interval.end}'
        return True, 'Valid'
    except Exception as e:
        return False, str(e)

valid, msg = validate_bed('input.bed')
print(f'{msg}')

Read BED Files

Python

import pybedtools

# Load BED file
bed = pybedtools.BedTool('input.bed')

# Iterate over intervals
for interval in bed:
    print(f'{interval.chrom}:{interval.start}-{interval.end}')
    print(f'Name: {interval.name}, Score: {interval.score}, Strand: {interval.strand}')

# Count intervals
n_intervals = bed.count()

# Convert to pandas DataFrame
df = bed.to_dataframe()

# Access specific columns
df = bed.to_dataframe(names=['chrom', 'start', 'end', 'name', 'score', 'strand'])

Filter BED Files

By Chromosome

# Single chromosome
grep "^chr1\t" input.bed > chr1.bed

# Multiple chromosomes
grep -E "^(chr1|chr2)\t" input.bed > chr1_2.bed

# Exclude chromosome
grep -v "^chrM\t" input.bed > no_chrM.bed

By Size

# Intervals >= 100bp
awk '($3 - $2) >= 100' input.bed > large.bed

# Intervals between 100-500bp
awk '($3 - $2) >= 100 && ($3 - $2) <= 500' input.bed > medium.bed

Python Filtering

import pybedtools

bed = pybedtools.BedTool('input.bed')

# Filter by chromosome
chr1 = bed.filter(lambda x: x.chrom == 'chr1')

# Filter by size
large = bed.filter(lambda x: len(x) >= 100)

# Filter by strand
plus_strand = bed.filter(lambda x: x.strand == '+')

# Filter by score
high_score = bed.filter(lambda x: float(x.score) >= 500)

# Chain filters
result = bed.filter(lambda x: x.chrom == 'chr1' and len(x) >= 100)
result.saveas('filtered.bed')

Convert Formats

BED to Other Formats

# BED to GFF
bedtools bed12togff -i input.bed > output.gff

# BED to FASTA (extract sequences)
bedtools getfasta -fi reference.fa -bed input.bed -fo output.fa

# BED to FASTA with names
bedtools getfasta -fi reference.fa -bed input.bed -name -fo output.fa

From VCF to BED

# Extract variant positions
bcftools query -f '%CHROM\t%POS0\t%END\n' input.vcf > variants.bed

# Or using awk (simpler for SNPs)
grep -v "^#" input.vcf | awk '{print $1"\t"$2-1"\t"$2}' > snps.bed

From BAM to BED

# Convert alignments to BED
bedtools bamtobed -i input.bam > alignments.bed

# BED12 for spliced alignments
bedtools bamtobed -i input.bam -split > spliced.bed

Interval Arithmetic Basics

import pybedtools

interval = pybedtools.create_interval_from_list(['chr1', '100', '200', 'peak1', '0', '+'])

# Access fields
print(interval.chrom)   # chr1
print(interval.start)   # 100 (int)
print(interval.end)     # 200 (int)
print(interval.name)    # peak1
print(interval.score)   # 0
print(interval.strand)  # +

# Get length
print(len(interval))    # 100

# Get fields list
print(interval.fields)  # ['chr1', '100', '200', 'peak1', '0', '+']

Make Windows - Create Genomic Intervals

CLI

# Fixed-size windows across genome
bedtools makewindows -g genome.txt -w 10000 > windows_10kb.bed

# Windows with step size (sliding windows)
bedtools makewindows -g genome.txt -w 10000 -s 5000 > sliding_10kb.bed

# Fixed number of windows per chromosome
bedtools makewindows -g genome.txt -n 100 > 100_windows_per_chr.bed

# Windows within BED regions
bedtools makewindows -b regions.bed -w 1000 > windows_in_regions.bed

# Add window ID
bedtools makewindows -g genome.txt -w 10000 -i winnum > numbered_windows.bed

# Source chromosome in name
bedtools makewindows -g genome.txt -w 10000 -i srcwinnum > windows_with_source.bed

Python

import pybedtools

# From genome file
windows = pybedtools.BedTool().window_maker(g='genome.txt', w=10000)

# Sliding windows
windows = pybedtools.BedTool().window_maker(g='genome.txt', w=10000, s=5000)

# From BED regions
bed = pybedtools.BedTool('regions.bed')
windows = pybedtools.BedTool().window_maker(b=bed.fn, w=1000)

windows.saveas('windows.bed')

Common BED Extensions

Format	Description	Columns
narrowPeak	ENCODE narrow peaks	BED6 + signalValue, pValue, qValue, peak
broadPeak	ENCODE broad peaks	BED6 + signalValue, pValue, qValue
bedGraph	Signal track	chr, start, end, value
bedpe	Paired intervals	chr1, s1, e1, chr2, s2, e2, name, score, strand1, strand2

Cleanup Temp Files

import pybedtools

# At end of script
pybedtools.cleanup()

# Or use context manager (auto-cleanup)
pybedtools.set_tempdir('/tmp/pybedtools')

Related Skills

• interval-arithmetic - intersect, subtract, merge operations
• gtf-gff-handling - annotation file parsing
• coverage-analysis - depth calculations
• alignment-files/sam-bam-basics - BAM to BED conversion