# 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
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Philippine Garret authoredd35910cd
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