In order to run mHapTk, some annotation files are needed, including CpG position files and chromosome size files. CpG position files can be downloaed from this page and chromosome size files can be downloaded from UCSC genome browser.
| Genome | CpG sites | chromosome size |
|---|---|---|
| hg19 | hg19_CpG.gz hg19_CpG.gz.tbi |
hg19.chrom.sizes |
| hg38 | hg38_CpG.gz hg38_CpG.gz.tbi |
hg38.chrom.sizes |
| mm9 | mm9_CpG.gz mm9_CpG.gz.tbi |
mm9.chrom.sizes |
| mm10 | mm10_CpG.gz mm10_CpG.gz.tbi |
mm10.chrom.sizes |
CpG annotation file for other genomes can be created by a convenient tool, as described in this page.