De Novo Small Variant Options

The following command line options are available for de novo small variant calling.

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--enable-joint-genotyping—Run the joint genotyping caller.

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--variant—Specify the gVCF input to the workflow.

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--pedigree-file—Specify the pedigree file to enable De Novo Calling if there is a trio present.

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--qc-snp-denovo-quality-threshold—Specify the minimum DQ value for a SNP to be considered de novo. The default value is 0.05.

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--qc-indel-denovo-quality-threshold—Specify the minimum DQ value for an indel to be considered de novo. The default value is 0.02.