mitochondria

mitochondria.sh

git clone https://github.com/seppinho/mutserve.git -b v1.3.4
wget https://github.com/seppinho/mutserve/releases/download/v1.3.4/mutserve-1.3.4.jar

export ref=mutserve/files/rCRS.fasta

bwa index $ref

bwa mem -M -t 4 $ref mt_R1.fq.gz mt_R2.fq.gz \
| samtools view -@ 4 -1 -o mt.bam

java -jar mutserve-1.3.4.jar analyse-local \
 --input mt.bam \
 --output variants.vcf \
 --reference $ref

mkdir haplogrep-v2.2.9
cd haplogrep-v2.2.9
wget https://github.com/seppinho/haplogrep-cmd/releases/download/v2.2.9/haplogrep.zip
unzip haplogrep.zip
cd ..

haplogrep-v2.2.9/haplogrep classify \
 --in variants.vcf --format vcf --out haplogroups.txt --extend-report