amrtester - resolve epi-alleles

Synopsis

$ dnmtools amrtester [OPTIONS] <input.bed> <input.epiread>

In addition to amrfinder, which uses a sliding window, the amrtester program tests for allele-specific methylation in a given set of genomic intervals. The program can be run like this:

$ dnmtools amrtester -o output.amr -c /path/to/genome.fa intervals.bed input.epiread

This program works very similarly to amrfinder, but does not have options related to the sliding window. This program outputs a score for each input interval, and when the likelihood ratio test is used, the score is the p-value, which can easily be filtered later.

Options

 -o, -output

The name of the output file. If no file name is provided, the output will be written to standard output. Due to the size of this output, a file should be specified unless the output will be piped to another command or program. The output file contains genomic intervals in BED format, with intervals corresponding to those provided as input.

 -c, -chrom

FASTA file or directory of chromosomes containing FASTA files [required]

 -i, -itr

max iterations

 -v, -verbose

print more run info

 -P, -progress

print more run info to STDERR while the program is running.

 -b, -bic

use Bayesian Information Criterion (BIC) to compare models