modBAM

The modBAM format is a BAM/SAM file that contains modified base information. Writing modified BAM files is useful for storing per-read modification information alongside the alignment data. Right now, Rastair only allows storing CpG methylation information, which is represented as 5-methylcytosine (5mC) on the C and G on the opposite strand.

Rastair supports two annotation formats:

1. the "standard" format using MM tags, as specified in The SAM tags reference version 4.5.
2. the "legacy" format using XM/XR/XG tags as used by DRAGEN and Bismark, as described in the Illumina docs.

Standard mode

Writes the MM and ML tags as specified by the Optional Fields Specification. This is the format expected by tools like modkit.

Change of read sequence

The read sequence in the modBAM file will differ from the read sequence in the input BAM file.

Since Rastair deals with reads from TAPS, methylated Cs are represented as Ts in the read sequence. However, both the MM tag specification and other tools like modkit expect the fundamental base to be in the read sequence. That means, for a methylated CpG, the read sequence should contain a C on the forward strand and a G on the reverse strand, with only the MM tag indicating the modification instead of the presence of a T or A in the sequence.

To be compatible with this, Rastair will rewrite the read sequence at methylated positions when writing the standard modBAM output.

Legacy mode

Writes XR/XG/XM tags as used by DRAGEN and Bismark. The XM tag marks methylated positions as Z, unmethylated target-base positions as z, and everything else as .. (The read sequence is not rewritten.)

Use this mode when downstream tools expect the legacy Bismark-style tags.