This protocol provides detailed instructions on Quality Control, EWAS, and CpG island signature discovery with Illumina Infinitum MethylationEPIC and Infinium Human Methylation 450K BeadChip data. R package minfi and caret was used in this analysis.
pysam - Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.