Bismark Methylation Extractor

Extract methylation data from deduplicated BAM files.

bismark_methylation_extractor \
    --bedGraph --gzip \
    -o <output_directory> <deduplicated.bam>

• Key options:

  • --bedGraph: Generates bedGraph file

  • --gzip: Compresses the output files.

• Output:

  • Generates .bismark.cov.gz files and methylation call data in CpG, CHG, and CHH contexts.

  • Generates bedGraph.gz file.

  • Also generates splitting_report.txt file.