Longread Variant Calling

Gallery / Realistic Pipelines

Dense long-read variant-calling pipeline (six lines, nine sections): exercises inter-section routing around non-connecting section boxes, cross-row feeds via the inter-row gap, same-line bundle coincidence, and a same-colour crossover bridge.

Mermaid source

%%metro title: Long-read Variant Calling
%%metro style: dark
%%metro directional: true
%%metro files: fastq_in | FASTQ
%%metro files: bam_in | BAM
%%metro files: ubam_in | uBAM
%%metro line: ubam | uBAM | #0570b0
%%metro line: fastq | FASTQ | #2db572
%%metro line: bam | BAM | #f5c542
%%metro line: other | Other | #ff8c00
%%metro line: snvvcf | SNV VCF | #e63946
%%metro line: svvcf | SV VCF | #9d4edd
%%metro legend: tl

graph LR
    subgraph preprocessing [Pre-processing]

        fastq_in[ ]
        bam_in[ ]
        ubam_in[ ]
        cat_fastq[cat FASTQ]
        samtools_merge[samtools\nmerge]
        minimap2_align[minimap2]
        samtools_sort_index[samtools\nsort/index]
        mosdepth[mosdepth]

        fastq_in -->|fastq| cat_fastq
        ubam_in -->|ubam| samtools_merge
        bam_in -->|bam| samtools_merge
        cat_fastq -->|fastq| minimap2_align
        samtools_merge -->|ubam| minimap2_align
        minimap2_align -->|bam| samtools_sort_index
        samtools_merge -->|bam| samtools_sort_index
        samtools_sort_index -->|bam| mosdepth
    end

    subgraph small_variants [Small variant calling]

        clair3[Clair3]
        deepvariant[Deepvariant]
    end

    subgraph cnv_calling [CNVs]

        ontspectre_cnvcaller[ont-spectre CNVCaller]
    end

    subgraph tr_calling [Repeats]

        longtr[LongTR]
        straglr[Straglr]
        trgt[TRGT]
    end

    subgraph phasing [Phasing]

        whatshap_phase[WhatsHap Phase]
        whatshap_haplotag[WhatsHap Haplotag]

        whatshap_phase -->|bam,snvvcf| whatshap_haplotag
    end

    subgraph structural_variants [Structural Variants]

        sniffles[Sniffles]
        cutesv[CuteSV]
        jasminesv_callers[Jasmine merge callers]

        sniffles -->|svvcf,bam| jasminesv_callers
        cutesv -->|svvcf,bam| jasminesv_callers
    end

    subgraph jointcalling [Joint Calling]

        jasminesv_samples[Jasmine merge samples]
        glnexus[GLNexus]
    end

    subgraph annotation [Annotation]

        vep[VEP]
        snpeff[SnpEff]
        annotsv[AnnotSV]
    end

    subgraph reports [Reports]

        geneyx[Geneyx]
        sv_report[SV Report]
    end


    %% Inter-section edges
    samtools_sort_index -->|bam| clair3
    samtools_sort_index -->|bam| deepvariant
    samtools_sort_index -->|bam| longtr
    samtools_sort_index -->|bam| straglr
    samtools_sort_index -->|bam| trgt

    mosdepth -->|other| ontspectre_cnvcaller

    straglr -->|other| geneyx

    clair3 -->|snvvcf| ontspectre_cnvcaller
    deepvariant -->|snvvcf| ontspectre_cnvcaller

    clair3 -->|bam,snvvcf| whatshap_phase
    deepvariant -->|bam,snvvcf| whatshap_phase

    clair3 -->|snvvcf| glnexus
    deepvariant -->|snvvcf| glnexus

    clair3 -->|snvvcf| vep
    deepvariant -->|snvvcf| vep

    whatshap_haplotag -->|bam| sniffles
    whatshap_haplotag -->|bam| cutesv
    whatshap_haplotag -->|bam| jasminesv_samples

    ontspectre_cnvcaller -->|other| geneyx

    sniffles -->|svvcf| jasminesv_samples
    sniffles -->|svvcf| vep
    sniffles -->|svvcf| snpeff
    sniffles -->|svvcf| annotsv
    sniffles -->|svvcf| geneyx

    cutesv -->|svvcf| jasminesv_samples
    cutesv -->|svvcf| vep
    cutesv -->|svvcf| snpeff
    cutesv -->|svvcf| annotsv
    cutesv -->|svvcf| geneyx

    jasminesv_callers -->|svvcf| jasminesv_samples
    jasminesv_callers -->|svvcf| vep
    jasminesv_callers -->|svvcf| snpeff
    jasminesv_callers -->|svvcf| annotsv
    jasminesv_callers -->|svvcf| geneyx
    jasminesv_callers -->|svvcf| sv_report

    snpeff -->|svvcf| sv_report
    annotsv -->|svvcf| sv_report

    glnexus -->|snvvcf| vep

CLI command

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

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