Python code for adding XM tag (methylation call string) to bisulfite bam file.
Both Single-end and paired-end are available.
Some bisulfite alignment tools do not provide XM tag. XM tag is required to compute levels of DNA methylation heterogeneity.
The input bam file must be indexed.
python XMtagger.py [reference genome file] [input bam file] [output bam file]
python XMtagger.py hg38.fa input.bam output.bam
For faster results, it is recommended to use the subcommand tag in Metheor.