Mutserve¶
Mutserve is a variant caller for the mitochondrial genome to detect homoplasmic and heteroplasmic sites in sequence data. It is used by haplocheck and mtDNA-Server.
Availability¶
Download mutserve for local usage here.
Quick Start¶
Mutserve requires sorted and indexed CRAM/BAM files as an input.
curl -sL mutserve.vercel.app | bash
./mutserve
Available Tools¶
Currently two tools are available.
- call calls homoplasmic and heteroplasmic positions.
- annotate annotates the mutserve variant file (generated with
mutserve call).
Mutserve Call¶
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 Annotate¶
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.txt
Parameters¶
| 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.
BAM Preperation¶
Mutserve is currently not focused on indel calling. Best Practice Pipelines include steps for BAM files preperation like local realignment around indels (GenomeAnalysisTK.jar -T RealignerTargetCreator, java -jar GenomeAnalysisTK.jar -T IndelRealigner) or BQSR (GenomeAnalysisTK.jar -T BaseRecalibrator). Please also have a look at the Mutect2 Pipeline.