---
name: "mCaller"
section: "1"
platform: "linux"
package: "mcaller"
version: "1.0.3+git20210624.b415090-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mCaller"
---

# mCaller(1)

find methylation in nanopore reads

## NAME

mCaller.py - find methylation in nanopore reads

## DESCRIPTION

*/usr/lib/python3/dist-packages/joblib/\_multiprocessing\_helpers*.py:53: UserWarning: \[Errno 13\] Permission denied.  joblib will operate in serial mode

- warnings.warn('%s.

  joblib will operate in serial mode' % (e,))

usage: mCaller \[-h\] (**-p** POSITIONS \| **-m** MOTIF) **-r** REFERENCE **-e** TSV **-f** FASTQ

-

  \[-t THREADS\] \[-b BASE\] \[-n NUM\_VARIABLES\] \[--train\] \[--training\_tsv TRAINING\_TSV\] \[-d MODELFILE\] \[-s SKIP\_THRESH\] \[-q QUAL\_THRESH\] \[-c CLASSIFIER\] \[--plot\_training\] \[-v\]

Classify bases as methylated or unmethylated

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **-p** POSITIONS, **--positions** POSITIONS

  file with a list of positions at which to classify bases (must be formatted as space- or tab-separated file with chromosome, position, strand, and label if training)

- **-m** MOTIF, **--motif** MOTIF

  classify every base of type **--base** in the motif specified instead (can be single one-mer)

- **-r** REFERENCE, **--reference** REFERENCE

  fasta file with reference aligned to

- **-e** TSV, **--tsv** TSV

  tsv file with nanopolish event alignment

- **-f** FASTQ, **--fastq** FASTQ

  fastq file with nanopore reads

- **-t** THREADS, **--threads** THREADS

  specify number of processes (default = 1)

- **-b** BASE, **--base** BASE

  bases to classify as methylated or unmethylated (A or C, default A)

- **-n** NUM\_VARIABLES, **--num\_variables** NUM\_VARIABLES

  change the length of the context used to classify (default of 6 variables corresponds to 11-mer context (6\*2-1))

- **--train**

  train a new model (requires labels in positions file)

- **--training\_tsv** TRAINING\_TSV

  mCaller output file for training

- **-d** MODELFILE, **--modelfile** MODELFILE

  model file name

- **-s** SKIP\_THRESH, **--skip\_thresh** SKIP\_THRESH

  number of skips to allow within an observation (default 0)

- **-q** QUAL\_THRESH, **--qual\_thresh** QUAL\_THRESH

  quality threshold for reads (default none)

- **-c** CLASSIFIER, **--classifier** CLASSIFIER

  use alternative classifier: options = NN (default), RF, LR, or NBC (non-default may significantly increase runtime)

- **--plot\_training**

  plot probabilities distributions for training positions (requires labels in positions file and **--train**)

- **-v**, **--version**

  print version