Methylation-Related BAM Tags

When --enable-methylation-calling is set to true, DRAGEN analyzes the alignments produced for the configured --methylation-protocol and generates a single output BAM file that includes methylation-related tags for all mapped reads. As in Bismark, reads without a unique best alignment are excluded from the output BAM. The added tags are as follows.

Tag	Brief Description	Description
XR:Z	Read conversion	For the best alignment, which base-conversion was performed on the read: CT or GA.
XG:Z	Reference conversion	For the best alignment, which base-conversion was performed on the reference: CT or GA
XM:Z	Methylation call	A byte-per-base methylation string.

The XM:Z (methylation call) tag contains a byte that corresponds to each base in the sequence of the read. Each position that does not involve a cytosine contains a period (.). Each position that does involve a cytosine contains a letter. The letter indicates the context (CpG, CHG, CHH, or unknown). The case indicates methylation. Methylated positions use upper-case and unmethylated positions use lower-case. The letters used at cytosine positions are as follows.

Character	Methylated?	Context
.	Not cytosine	Not cytosine
z	No	CpG
Z	Yes	CpG
X	No	CHG
X	Yes	CHG
h	No	CHH
H	Yes	CHH
u	No	Unknown
U	Yes	Unknown