Workflow Steps and Code Snippets

1107 tagged steps and code snippets that match keyword gatk

WES analysis pipeline

shell:
    """
    gatk Mutect2 -R {input.ref} -I {input.tumor} \
        -tumor {params.tumor} -O {output.vcf} \
        --germline-resource {input.germ_res} \
        --f1r2-tar-gz {output.f1r2tar} \
        -L {input.interval} \
        -ip 100 \
        {params.normal_input} {params.normalname} \
        {params.pon} {params.extra}
    """

SnakeMake gatk From line 27 of rules/calling.smk

shell:
    """
    gatk LearnReadOrientationModel {params.i} -O {output}
    """

SnakeMake gatk From line 47 of rules/calling.smk

shell:
    """
    gatk GetPileupSummaries -I {input.bam} -V {input.germ_res} \
        -L {input.germ_res} -O {output}
    """

SnakeMake gatk From line 59 of rules/calling.smk

shell:
    """
    gatk CalculateContamination -I {input.tumor}  \
        {params.matched} \
        -O {output}
    """

SnakeMake gatk From line 73 of rules/calling.smk

shell:
    """
    gatk MergeVcfs {params.i} -O {output.vcf}
    """

SnakeMake gatk From line 88 of rules/calling.smk

shell:
    """
    gatk MergeMutectStats {params.i} -O {output.stats} 
    """

SnakeMake gatk From line 101 of rules/calling.smk

shell:
    """
    gatk FilterMutectCalls -V {input.vcf} -R {input.ref} \
        --contamination-table {input.contamination} \
        --stats {input.stats} \
        -ob-priors {input.f1r2model} \
        -O {output.vcf} \
        {params.extra}
    """

SnakeMake gatk From line 120 of rules/calling.smk

shell:
    """
    gatk SelectVariants -V {input.vcf} \
        -R {input.ref} \
        -O {output.vcf} \
        --exclude-filtered \
        -OVI
    """

SnakeMake gatk From line 139 of rules/calling.smk

shell:
    """
    gatk Mutect2 \
        -I {input.bam} \
        -R {input.ref} \
        -O {output.vcf} \
        -L {input.intervals} \
        -ip 100 \
        --max-mnp-distance 0
    """

SnakeMake gatk From line 15 of rules/pon.smk

shell:
    """
    gatk GenomicsDBImport \
        -R {input.ref} \
        --genomicsdb-workspace-path {output} \
        -V {params.vcfs} \
        -L {input.intervals} \
        -ip 100
    """