Discovery of Nuclear Mitochondrial Insertions (dinumt)

Description

This software is designed to identify and genotype nuclear insertions of mitochondrial origin from whole genome sequence data. It consists of two programs: dinumt (di-nu-mite), which identifies sites of insertions in a single sample and gnomit (geno-mite), which genotypes those sites across multiple samples. There is an additional program named clusterNumtsVcf which will merge sites identified in multiple samples into a single merged file for genotyping.

Required third-party resources

A number of third party software packages are required by these programs:

• samtools: http://samtools.sourceforge.net/
• exonerate: http://www.ebi.ac.uk/~guy/exonerate/
• vcftools: http://vcftools.sourceforge.net/
  • you will need to make sure Vcf.pm is in your perl library path

In addition, you will need:

• reference genome in fasta format (e.g. hs37d5.fasta)
• individual MT sequence (e.g. MT.fa or chrM.fa)
• bed file of annotated numts in reference (refNumts.bed for hg19 is included in package)

The genotyping step requires the use of a sample index file containing various sample-level information (mean insert size, coverage, etc). A template has been provided, and the relevant data can be obtained by using GATK (DepthOfCoverage walker) and Picard (CollectInsertSizeMetrics) or custom scripts. If you are running dinumt in cram files under reference genome version GRCh38, please use the corresponding .pl in the folder.

Parameters

Additional information about various parameters below:

• --len_cluster_include : width of window to consider anchor reads as part of the same cluster, typically calculated as mean_insert_size + 3 * standard_deviation
• --len_cluster_link : width of window to link two clusters of anchor reads in proper orientation, typically calculated as 2 * len_cluster_include
• --max_read_cov : maximum read depth at potential breakpoint location, used to filter out noisy regions of the genome, typically calculated as 5 * mean_coverage
• --output_support : output all sequence reads supporting an insertion event in SAM format to filename in --support_filename option
• --mask_filename : bed file of all numts annotated in reference sequence, one is provided for GRCh37 but additional versions can be obtained from UCSC Genome Browser
• --min_map_qual : mininum mapping quality required for anchor read to be considered for cluster support, default is 10 but can be adjusted as needed

Example workflow

An example workflow would be as follows:

dinumt.pl \
--mask_filename=refNumts.bed \
--input_filename=sample1.bam \
--reference=hs37d5.fa \
--min_reads_cluster=1 \
--include_mask \
--output_filename=sample1.vcf \
--prefix=sample1 \
--len_cluster_include=577 \
--len_cluster_link=1154 \
--insert_size=334.844984 \
--max_read_cov=29 \
--output_support \
--support_filename=sample1_support.sam

grep ^# sample1.vcf > header.txt
cat *vcf | grep -v ^# | vcf-sort.pl | clusterNumtsVcf.pl --reference=hs37d5.fa > data.txt
cat header.txt data.txt > merged.vcf

(merged vcf can be split into smaller pieces with multiple sets of sites run in parallel, if need be)

gnomit.pl \
--input_filename=merged.vcf \
--mask_filename=refNumts.bed \
--info_filename=sampleInfo \
--output_filename=merged_geno.vcf \
--samtools=samtools \
--reference=hs37d5.fa \
--breakpoint \
--min_map_qual=13 \
--dir_tmp=/tmp \
--exonerate=exonerate \
--mt_filename=MT.fa

Citation

• Dayama, Gargi, Weichen Zhou, Javier Prado-Martinez, Tomas Marques-Bonet, and Ryan E. Mills. 2020. Characterization of Nuclear Mitochondrial Insertions in the Whole Genomes of Primates, NAR Genomics and Bioinformatics, 2020, lqaa089,. https://doi.org/10.1093/nargab/lqaa089

• Dayama, Gargi, Sarah B Emery, Jeffrey M Kidd, and Ryan E. Mills. 2014. The genomic landscape of polymorphic human nuclear mitochondrial insertions, Nucleic Acids Research, 2014, gku1038, https://doi.org/10.1093/nar/gku1038

Contact

Questions: Please contact Ryan Mills at remills@umich.edu 04/16/2014