I am using GATK v2 (GenomeAnalysisTK-2.0-0-g4c0ffd4) and was trying out the new BaseRecalibrator walker. According to this post the BaseRecalibrator should output "A PDF file containing quality control plots showing the patterns of recalibration of the data", however I do not have any such file. Both the BaseRecalibrator and PrintReads steps of the BQSR pipeline appear to have worked as I have a recalibrated BAM file and the accompanying GATKReport but I would like to be able to view plots of the recalibration process (and preferably have these generated automatically by the recalibration pipeline).
Can you please help? Thanks
