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.

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.