Using Bismark for Methylation Calling

The recommended approach to methylation calling is to automate the multiple required alignment runs, and add the XM, XR, XG tags. To generate a separate BAM file for each of the constraints and conversions needed by the methylation protocol, set ‑‑enable-methylation-calling to false. The BAM files can be used as input into Bismark for methylation calling. Contact Illumina Technical Support for more information on this use case if desired.

In this mode, a single DRAGEN run produces multiple BAM files in the directory specified by ‑‑output-directory, each containing alignments in the same order as the input reads. It is not possible to enable sorting or duplicate marking for these runs. Alignments include MD tags and have /1 or /2 appended to the names of paired-end reads for Bismark-compatibility. The BAM files use the following naming conventions:

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Single-end reads—output-directory/output-file-prefix.{CT,GA}read{CT,GA}reference.bam

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Paired-end-reads—output-directory/output-file-prefix.{CT,GA}read1{CT,GA}read2{CT,GA}reference.bam,

Where output-directory and output-file-prefix are specified by the corresponding options, and CT and GA correspond to the base conversions listed in the table above.

Bismark does not have a directional-complement mode, but you can process such samples using Bismark’s nondirectional mode with the expectation that runs 1 and 2 produce very few good alignments.