Table 3:

Reads2Map workflows default option set based on tests with empirical and simulated data

Process	Workflow options	Default
SNP calling	Run GATK	TRUE
	Run Freebayes	FALSE
	Run Stacks	TRUE
	Run TASSEL	FALSE
	Remove duplicates	FALSE
	Replace AD by BAM counts	FALSE
	GATK hard filters	TRUE
genotype calling	Replace AD by missing when GT is missing	TRUE
	Probability threshold	0.8
	Run updog	TRUE
	Run polyRAD	TRUE
	Run SuperMASSA	FALSE
	Run GUSMap	FALSE
linkage map	Filter noninformative	TRUE
	Add multiallelics	TRUE (if available)
	Global errors	0.05
	Genotype caller probabilities	FALSE
	Genotype caller probabilities + global errors	0.05