nf-core/variantprioritization

Somatic and germline variant prioritization using PCGR and CPSR. GitHub

Mermaid source

%%metro title: nf-core/variantprioritization
%%metro file: cna_in | CNA
%%metro file: vcf_in | VCF
%%metro file: report_pcgr | HTML
%%metro file: report_cpsr | HTML
%%metro line: somatic | Somatic | #4CAF50
%%metro line: germline | Germline | #9923A0
%%metro line: reference | Reference | #2196F3

graph LR

    subgraph preprocessing [Pre-processing of vcf files]
        vcf_in[ ]
        tabix[tabix]
        bcftools_norm[bcftools/norm]
        bcftools_filter[bcftools/filter]

        vcf_in -->|somatic,germline| tabix
        tabix -->|somatic,germline| bcftools_norm
        bcftools_norm -->|somatic,germline| bcftools_filter
    end

    subgraph format_files [Prepare files for PCGR]
        reformat_vcf[Reformat VCF]
        intersect[Intersect VCF]
        prepare_pcgr[Prepare VCF]
        cna_in[ ]
        reformat_cna[Reformat CNA]

        reformat_vcf -->|somatic| intersect
        reformat_vcf -->|somatic| prepare_pcgr
        intersect -->|somatic| prepare_pcgr
        cna_in -->|somatic| reformat_cna
    end

    subgraph get_reference [Reference]
        get_pcgr[PCGR DB]
        get_vep[VEP Cache]
    end

    subgraph run_pcgr [PCGR]
        pcgr[PCGR]
        report_pcgr[ ]

        pcgr -->|somatic| report_pcgr
    end

    subgraph run_cpsr [CPSR]
        cpsr[CPSR]
        report_cpsr[ ]

        cpsr -->|germline| report_cpsr
    end

    %% Inter-section edges
    get_pcgr -->|reference| cpsr
    get_vep -->|reference| cpsr
    bcftools_filter -->|germline| cpsr
    bcftools_filter -->|somatic| reformat_vcf
    reformat_cna -->|somatic| pcgr
    prepare_pcgr -->|somatic| pcgr
    get_pcgr -->|reference| pcgr
    get_vep -->|reference| pcgr

CLI command

nf-metro render examples/variantprioritization.mmd -o variantprioritization.svg

Rendered map