genome-maps - An open-source high-performance web-based HTML5 genome browser. Genome Maps can be customized and allow browsing user data such as BAM and VCF files among other formats.
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.
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.