gatk_xsede

infile_ this is the ref file
gatkref_dict_ this is the .dict file (mandatory)
gatkref_fai_ this is the .fai file (mandatory)
gatk_sortedbam_ this is the sortedbam file (mandatory for step 1)
gatk_sortedbamindex_ this is the .bai file (mandatory)
indelrealign_inf_ this is the .intervals file (required for runs starting with step 2.
vcf_inf_ this is the indel realign.bam file (required for runs starting with step 3)

       
<!-- Visible parameters -->
runtime_ = (float) up to 168 hours, default = 0.25
gatk_real_ = (switch) default=1 Run realignertarget command
gatk_indelreal_ = (swtich) default=1 Run indelrealignertarget command
gatk_gvcf_ = (switch) default=1 Run GVCF command