We designed a novel probabilistic model to infer allele-specific DNA methylation (ASM) based on data from high-throughput BS-seq experiments. This model is independent of genotype, and therefore has broad applicability to identify ASM in the context of imprinting. In essence, our model describes the degree to which methylation states in reads appear to reflect two distinct patterns, each pattern representing roughly half the data. Our method only requires formatted mapped reads (Epiread format) as input, and reports all possible regions of ASM in the genome.

System requirements

64-bit machine, GCC version >= 4.1, and GSL version 1.15 available here.

Installation

amrfinder is now a part of the MethPipe Package. Please see the MethPipe homepage for installation details.

Quick usage guide

Here are examples showing how to run the programs in the amrfinder package. A much more detailed explanation can be found in the methpipe manual under the amrfinder section.

methstates is used to convert the mapped reads file into a special format called `Epiread’ format, which consists of three columns. The first column is the chromosome of the read, the second column is the numbering order of the first CpG in the read, and the last column is the CpG-only sequence of the read. A usage example is shown below:

$ methstates -c /path/to/hg38_chroms Human_test.mr -o Human_test.epiread

Option -c indicates the folder of corresponding chromosomes.

amrfinder scans the genome using a sliding window to identify AMRs. The following command shows an example to run the program.

$ amrfinder -o Human_test_AMR.bed -i 10 -w 10 -m 1 -b \
  -c /path/to/hg38_chroms Human_test.mr

Citation

Fang F, Hodges E, Molaro A, Dean MD, Hannon GJ and Smith AD (2012)
The genomic landscape of human allele-specific DNA methylation
PNAS [PDF][Publisher Site]