[DEFAULT]
jar: ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar
referenceRoot: /home/radon01/depristo/work/humanref/Homo_sapiens_assembly18
reference: %(referenceRoot)s.fasta
referenceIndex: %(reference)s.fai
referenceDict: %(referenceRoot)s.dict
java: java
jvm_args: -ea -Xmx2048m
gatkData: /humgen/gsa-scr1/GATK_Data
dbsnp: %(gatkData)s/dbsnp_129_hg18.rod
tmp: /tmp/
args: -l INFO
Sting: ~/dev/GenomeAnalysisTK/trunk
#args: -l INFO -L chr1:1-1,000,000

[CountCovariates]
args: --MIN_MAPPING_QUALITY 1 -D %(dbsnp)s

[TableRecalibration]
args: -compress 1

[R]
Rscript: /broad/tools/apps/R-2.6.0/bin/Rscript 
PlotQEmpStated: %(Sting)s/R/plot_q_emp_stated_hst.R
PlotQDiffByCycle: %(Sting)s/R/plot_qual_diff_v_cycle.R
PlotQDiffByDinuc: %(Sting)s/R/plot_qual_diff_v_dinuc.R