+ - prefix: "-R"
+ valueFrom: $(inputs.reference)
+ - prefix: "-I"
+ valueFrom: $(inputs.bam)
+ - prefix: "-O"
+ valueFrom: $(runtime.outdir)/$(inputs.sample).gatk.g.vcf.gz
+ - prefix: "-ERC"
+ valueFrom: "GVCF"
+ - prefix: "-GQB"
+ valueFrom: "5"
+ - prefix: "-GQB"
+ valueFrom: "20"
+ - prefix: "-GQB"
+ valueFrom: "60"