MitoMut

MitoMut identifies mitochondrial deletions from paired-end next generation sequencing (NGS) data.

Citation

If our work is useful to you, please cite:
C. Shane Elder and Catherine E. Welsh. MitoMut: An Efficient Approach to Detecting Mitochondrial DNA Deletions from Paired-end Next-generation Sequencing Data. Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Health Informatics, 2019.

@inproceedings{inproceedings,
  author = {Elder, C. Shane and Welsh, Catherine},
  year = {2019},
  month = {09},
  pages = {177-182},
  title = {MitoMut: An Efficient Approach to Detecting Mitochondrial DNA Deletions from Paired-end Next-generation Sequencing Data},
  isbn = {978-1-4503-6666-3},
  doi = {10.1145/3307339.3342158}
}

Dependencies

To run MitoMut, you need the following dependencies:

1. python2.7+ or python3.0+
   
2. PySam (Python Module that must be downloaded into your version of Python)
   
3. Samtools (must be on environment path)
   
4. BLAT (must be on environment path) (available at http://hgdownload.soe.ucsc.edu/admin/exe/)
   

To check the presence of dependencies, cd into MitoMut's directory and run python check_dependencies.py on your environment's command line or terminal.

Instructions

MitoMut Usage:
python MitoMut.py [-f/-c/-s/-si/-e/-l] *.bam

Note– Flags may go in any order. If they require an argument, it must
come directly after the flag.

-h: This flag shows the help screen with all optional flags and usage information.
-c: This flag specifies the header for the mitochondrial section of the genome.
-f: This flag specifies the path to fasta reference genome
-d: Sets the write directory for all intermediate and result files
-e: Use this flag if the reference genome is a whole genome reference rather than
mitochondrial only.
-q: Sets the minimum quality score to be considered a deletion
-s: Sets the minimum number of reads required to support a deletion
-l: Sets the length of the mitochondrial genome (only use if not human)
-si: sets the minimum number of deleted bases required to be qualified as a deletion

Flag Defaults:

-c: MT
-f: mt.fasta (supplied when downloading MitoMut)
-q: 30
-s: 5
-si: 5
-l: 16569
-d: .

Sample Runs

(Do not type what is in parentheses)

python MitoMut.py test.bam (A standard run with no extra configuration)
python MitoMut.py -c chrM test.bam (The bam file's mitochondrial header is chrM instead of MT)
python MitoMut.py -d /Users/example_user/ test.bam (Writing to a different directory than where the bam file is)
python MitoMut.py -e -f genome.fasta test.bam (extracting the mitochondrial portion of the reference genome)
python MitoMut.py -s 20 test.bam (Only deletions with at least 20 supporting reads will be reported)

Test Installation (Works on any Unix based operating system)

Once unzipped, test your installation with the following steps:

1. cd into MitoMut's download directory
   
2. Check your dependencies: python ./check_dependencies.py
   
3. If all dependencies are installed: python ./MitoMut.py -f mt.fasta -c chrM test.bam
   
4. Check the output files: diff test_results.txt test.bam_results.txt
   
5. If diff displays nothing, all is successful!