# Mitochondria pipeline README
2019-06-06


## Pre-requisites
This pipeline requires docker.
GRCh38 reference file needs to be loaded in </path/to/references/directory>, decompressed, indexed by BWA and SequenceDictionary generated by picard tools. The GRCh38 genome version is mandatory (you can not use hg19). You can download it from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
samples.R1.fastq.gz and sample.R2.fastq.gz files need to be loaded in <path/to/fastq/gz/samples/files/directory> without subfolder. Each sample needs to be sequenced in paired-end.

## Hardware requirements
We strongly recommend a computer with at least:
- Memory 16 Go.
- CPU 2 to 16 cores.
- 30 Go disk space.

## Download Pipeline
We provide a docker version for local usage. Download docker image pipelinemitov1.tar (http://gitlab.gad-bioinfo.org/gad-public/pipelinemito)


## Load and run pipeline  
Commands:
	docker load -i pipelinemitov1.tar
	docker run  -v </path/to/fastq/gz/samples/files/directory>:/data:rw -v </path/to/references/directory>:/mitopipeline:ro --env THREAD=<int> --env REFNAME=<ref.fa> pipelinemitov1

Example: 
	docker load -i pipelinemitov1.tar
	docker run  -v /data/docker-data:/data:rw -v /data/docker-references:/mitopipeline:ro --env THREAD=2 --env REFNAME=grch38.fa pipelinemitov1


## Input File Format
The input format is fastq.gz. 


## Output Files Formats
The ouput formats are TSV and VCF.
Each variants is annotated with:
- Chromosome
- Position
- Reference and alternative alleles
- Genomic change
- Filters flags:  Is the variant synonymous (SYN)? frequent in GenBank (FM)? frequent in our cohort (FB)? determining patient haplogroup (HPG)? Or is not filtered (PASS)?
- Genotype (0/0, 0/1, 1/1)
- Genbank frequency (0 to 100.0%)
- Haplogroups defined by the variant
- Heteroplasmy rate (0 to 100.0%)
- MitoTIP score hen available (0 to 100.0%)

TSV report contains all mitochondria variants flagged "PASS". 


## Cite

## Contact