dbsnp_rod_file=/path/to/dbsnp/file
dcov_value=3000
gatk_jar_file=/opt/biotools/GenomeAnalysisTK/GenomeAnalysisTK.jar
indels_file=/path/to/indels/file.bed
picard_jar_file=/projects/stsi/tools/picard/latest/MarkDuplicates.jar
queue_size=150
reference_fasta_file=/path/to/ref/file
stand_call_conf=50.0
stand_emit_conf=10.0
glm_arg=BOTH