Version Compatibility

Reference examples tested with: 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.

Methylation Calling

"Extract methylation calls from my Bismark BAM" → Generate per-cytosine methylation reports (CpG, CHG, CHH contexts) from aligned bisulfite sequencing data.

• CLI: bismark_methylation_extractor --bedGraph --cytosine_report sample.bam

Basic Extraction

# Extract methylation calls from Bismark BAM
bismark_methylation_extractor --gzip --bedGraph \
    sample_bismark_bt2.bam

Paired-End Extraction

bismark_methylation_extractor --paired-end --gzip --bedGraph \
    sample_bismark_bt2_pe.bam

Common Options

bismark_methylation_extractor \
    --paired-end \                 # For paired-end data
    --gzip \                       # Compress output
    --bedGraph \                   # Generate bedGraph file
    --cytosine_report \            # Genome-wide cytosine report
    --genome_folder /path/to/genome/ \  # Required for cytosine_report
    --buffer_size 10G \            # Memory buffer
    --parallel 4 \                 # Parallel extraction
    -o output_dir/ \
    sample.bam

CpG Context Only

# Most common - extract only CpG methylation
bismark_methylation_extractor \
    --paired-end \
    --no_overlap \                 # Avoid double counting overlapping reads
    --gzip \
    --bedGraph \
    --CX \                         # Also extract CHG/CHH (optional)
    sample.bam