I cannot produce BQSR plots, although I can open the grp file with gsa.read.gatkreport.
Here's the command:
java -Xmx1g -jar $shares/GenomeAnalysisTK-2.3-6-gebbba25/GenomeAnalysisTK.jar \
-T BaseRecalibrator \
-I ./0.reorder.bam \
-R $shares/ftp.broadinstitute.org/bundle/2.3/hg19/ucsc.hg19.fasta \
-knownSites $shares/ftp.broadinstitute.org/bundle/2.3/hg19/dbsnp_137.hg19.vcf \
-BQSR ./0.reorder.bam.recal.grp \
-o ./0.reorder.bam.post_recal.grp \
--plot_pdf_file ./0.reorder.bam.post_recal.grp.pdf \
-L chr1:1-1000 \
-l DEBUG \
--intermediate_csv_file ./0.reorder.bam.post_recal.grp.csv
##### ERROR stack trace
java.lang.NullPointerException
at org.broadinstitute.sting.utils.Utils.join(Utils.java:286)
at org.broadinstitute.sting.utils.recalibration.RecalUtils.writeCSV(RecalUtils.java:450)
at org.broadinstitute.sting.utils.recalibration.RecalUtils.generateRecalibrationPlot(RecalUtils.java:394)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.generatePlots(BaseRecalibrator.java:474)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.onTraversalDone(BaseRecalibrator.java:464)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.onTraversalDone(BaseRecalibrator.java:112)
at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:97)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
It looks like the csv file is not being produced.
Thanks!
