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 corresponding to each base in the read’s sequence. There is a period (‘.’) for each position not involving a cytosine, and a letter at cytosine positions. The letter indicates the context (CpG, CHG, CHH, or unknown). The case indicates methylation, with upper-case positions being methylated and lower-case unmethylated. 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