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Mutserve is a library to detect heteroplasmic and homoplasmic sites in mtDNA NGS data. It has been integrated in mtDNA-Server. For scalability reasons, mutserve is parallelized using Hadoop MapReduce but also available as a standalone tool.

You can run mutserve as a standalone tool starting with CRAM/BAM files and detecting heteroplasmic and homoplasmic sites. By default BAQ is set (--noBaq otherwise).

Please be aware that mutserve always reports the non-reference level as the heteroplasmy level, while mtDNA-Server reports the minor component.

wget https://github.com/seppinho/mutserve/releases/download/v1.1.17/mutserve-1.1.17.jar

java -jar mutserve-1.1.17.jar  analyse-local --input <file/folder> --output <filename.vcf / filename.txt> --reference <fasta> --level 0.01

To create a VCF file as an output simple specify --output filename.vcf.gz. Please use this reference file when using BAQ.

By default (--output filename does not end with .vcf or .vcf.gz) we export a TAB-delimited file including ID, Position, Reference, Variant & VariantLevel. Please note that the VariantLevel always reports the non-reference variant level. The output file also includes the most and second most base at a specific position (MajorBase + MajorLevel, MinorBase+MinorLevel). The reported variant can be the major or the minor component. The last column includes the type of the variant (1: Homoplasmy, 2: Heteroplasmy or Low-Level Variant, 3: Low-Level Deletion, 4: Deletion, 5: Insertion). See here for an example.

If you want a VCF file as an output, please specify --output filename.vcf.gz. Heteroplasmies are coded as 1/0 genotypes, the heteroplasmy level is included in the FORMAT using the AF attribute (allele frequency) of the first non-reference allele. Please note that indels are currently not included in the VCF. This VCF file can be used as an input for https://github.com/seppinho/haplogrep-cmd.

• We currently report homoplasmies only with a coverage of (FWD+REV)/2 >= 30.
• The insertions/deletions calling is currently in beta, there is currently no normalization or realignment applied for indel positions.

If you have a mixture model generated, you can use mutserve for checking precision, specificity and sensitivity. The expected mutations (homoplasmic and heteroplasmic) need to be provided as gold standard in form of a text file, with one column, containing the positions expected. The variant from analyse-local are used as input file and length needs to be specified (usually 16,569, but as there are different reference sequence, this can vary as well).

java -jar mutserve-1.1.17.jar  performance --in <variantfile> --gold <expectedmutations> --length <size of reference>

If you use this tool, please cite this paper.

• git clone https://github.com/seppinho/mutserve
• Import Maven project into your favourite IDE
• maven install