mutect2_pon.inputs.json

{
	"Mutect2_Panel.pon_name":"panel_of_normal",
	"Mutect2_Panel.normal_bams":"Array[File]",
	"Mutect2_Panel.normal_bais":"Array[File]",
	
	"Mutect2_Panel.ref_fasta":"gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta",
	"Mutect2_Panel.ref_fai":"gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai",
	"Mutect2_Panel.ref_dict":"gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.dict",
	"Mutect2_Panel.scatter_count":10,

	"Mutect2_Panel.intervals":"gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list",
	"Mutect2_Panel.Mutect2.variants_for_contamination":"gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf",
	"Mutect2_Panel.gnomad":"gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf",

	"Mutect2_Panel.gatk_docker":"broadinstitute/gatk:4.1.4.0"
}