27 lines
777 B
INI
Executable File
27 lines
777 B
INI
Executable File
[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
|