The Detect QIAseq Methylation workflow calls methylation levels on targeted data.
It can be found here:
Ready-to-Use Workflows | QIAseq Panel Analysis | Detect QIAseq Methylation
The workflow takes as input reads sequenced with a QIAseq Targeted Methyl Panel kit. For convenience, process several samples at once using the batch mode highlighted in figure 7.1. Note that only Illumina paired-end sequencing is supported by this workflow at this point.
QIAseq panels are designed to use hg19 as reference, but custom panels can be designed against either hg19 or GRCh38. Custom primers can be obtained through the "QIAseq Methyl Panel Primer Files with primer 3' Location (GRCh37/GRCh38)" option of this webpage: http://mars.sabiosciences.com/sapims/ngs_qiaseq_DNA_custom.php, and imported with the Import QIAGEN Primer tool.