dbsnp_rod_file=/path/to/dbsnp/file
dcov_value=3000
gatk_jar_file=/projects/stsi/tools/gatk/latest/GenomeAnalysisTK.jar
indels_file=
picard_jar_file=/projects/stsi/tools/picard/latest/MarkDuplicates.jar
# system-defined number of jobs that can be running in a user gueue at any time
queue_size=150
reference_fasta_file=/path/to/ref/file
stand_call_conf=50.0
stand_emit_conf=10.0
chr_len_file=/projects/stsi/data/GRCh37/GRCh37_p2/BWA_index/GRCh37.chr1_22_XYMT_unplaced_unlocalized.len
# number of slots to keep open during gatk_pipeline run for other jobs
queue_buffer_size=5
# number of base pairs to process in a single gatk job (used to set args for -L option)
partition_size=10000000