Mutserve2
Mutserve2 is a variant caller for the mitochondrial genome to detect homoplasmic and heteroplasmic sites in sequence data.
For easier execution and pre- and postprocessing steps, mutserve2 has been integrated into the mtDNA-Server 2
Quick Start
Mutserve requires sorted and indexed CRAM/BAM files as an input.
curl -sL mutserve.vercel.app | bash
./mutserveDocumentation
Available Tools
Currently two tools are available.
- call: Variant Calling of homoplasmic and heteroplasmic positions.
- annotate: Annotation of mutserve variants (generated with
mutserve call).
Mutserve Variant Calling
wget https://github.com/seppinho/mutserve/raw/master/test-data/mtdna/bam/input/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
curl -sL mutserve.vercel.app | bash
./mutserve call --reference rCRS.fasta --output HG00096.vcf.gz --threads 4 *.bam Please use this reference file when using BAQ (disabled by default since v2.0.0).
Mutserve Annotation
Mutserve allows to annotate the variant file (.txt) with a predefined annotation file
./mutserve annotate --input variantfile.txt --annotation rCRS_annotation_2020-08-20.txt --output AnnotatedVariants.txtParameters
| Parameter | Default Value / Comment | Command Line Option |
|---|---|---|
| Input Files | sorted and indexed BAM/CRAM files | |
| Output Name | output file; supported: *.txt, *.vcf, *vcf.gz | --output |
| Reference | reference file | --reference |
| Threads | 1 | --threads |
| Minimum Heteroplasmy Level | 0.01 | --level |
| Define specific mtDNA contig in whole-genome file | null | --contig-name |
| Output Fasta | false | --writeFasta |
| Output Raw File | false | --writeRaw |
| MappingQuality | 20 | --mapQ |
| BaseQuality | 20 | --baseQ |
| AlignmentQuality | 30 | --alignQ |
| Enable Base Alignment Quality (BAQ) | false | --baq |
| Disale 1000 Genomes Frequence File | false | --noFreq |
| Call deletions (beta) | false | --deletions |
| Call insertions (beta) | false | --insertions |
| Disable ANSI output | --no-ansi |
|
| Show version | --version |
|
| Show help | --help |
Output Formats
Tab delimited File
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.
VCF
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.
Limitations
The focus of mutserve is currenly on SNP calling and not on indels. Please checkout mtDNA-Server 2 to combine SNV with InDel Calling.
Contact
Citation
Weissensteiner H, Forer L, Fendt L, Kheirkhah A, Salas A, Kronenberg F, Schoenherr S. 2021. Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 31: 309-316
Weissensteiner H, Forer L, Fuchsberger C, Schöpf B, Kloss-Brandstätter A, Specht G, Kronenberg F, Schönherr S. 2016. mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud. Nucleic Acids Res 44: W64–9.