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Add ploidy to germline_detect_variants and pass along to GATK GenotypeGVCFs and HaplotypeCaller

@jasonwalker80 jasonwalker80 changed the title GATK ploidy input for Germline SNV/Indels Non-human WGS Pipeline with Basic QC and Variant Calls (SNVs/Indels) Jun 18, 2019
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