⛔️ DEPRECATED!!!
- Please use Mutserve for variant calling https://github.com/seppinho/mutserve
- or HaploCheck for contamination detection https://github.com/genepi/haplocheck
Be aware of the limitations when using the outdated Tools:
- splitter - Split mitochondrial variants and heteroplasmies from mtDNA-Server
- contChecker - Compare mitochondrial profiles from extended report in HaploGrep 2
- lofreq - Split mitochondrial variants according the VCF file generated with LoFreq as Variant file (txt)
- bam2var - naive variant caller (input BAM file, output Variant file txt)
- haplochecker - check for contamination in mtDNA NGS data (BAM file) based on Phylotree 17
java -jar mitolib-0.1.2.jar haplochecker --in Bamfile.bam --out outputfolder --ref rCRS.fasta
--QUAL 20 --MAPQ 200 --VAF 0.01- haplochecker2 - check for contamination in mtDNA-Server raw data (large txt.file) based on Phylotree 17
java -jar mitolib-0.1.2.jar haplochecker2 --in raw.txt --out outputfolder --VAF 0.01