Annotation files for mHapTk

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.

For Human and Mouse

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

For other genomes

CpG annotation file for other genomes can be created by a convenient tool, as described in this page.