Using TAPS Support

TET-Assisted Pyridine Borane Sequencing (TAPS) is a new assay which directly converts methylated C to T, whereas typical bisulfite conversion converts unmethylated C to T. This approach preserves genomic complexity and uses less destructive chemicals to enable lower input DNA.

To enable analysis of FASTQ data generated through TAPS, set --methylation-TAPS to true. By default, the option is false. This option is performed only during the alignment step and is not necessary when generating methylation cytosine and M-Bias reports from an existing BAM.