I'm trying to run AnalyzeCovariates to produce calibration plots, but not getting a PDF, so I decided to upgrade my R installation and all the packages required (gsalib, ggplot2, etc). Now I'm getting the following error:
ERROR MESSAGE: Bad input: The GATK report has an unknown/unsupported version in the header: %PDF-1.4
I'm using GATK version 2.8-1-g932cd3a.
Here's the command I'm running:
java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates \ -R /path/genome.fa \ -L /path/genome.interval_list \ -before recal1.table \ -after recal2.table \ -plots recal.pdf \ -csv recal.csv
I'm using the latest version of R and all the packages. Here's my R
> sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  C attached base packages:  grid tools stats graphics grDevices utils datasets  methods base other attached packages:  gsalib_2.0 reshape_0.8.4 plyr_1.8  gplots_2.12.1 ggplot2_0.9.3.1 BiocInstaller_1.12.0 loaded via a namespace (and not attached):  KernSmooth_2.23-10 MASS_7.3-29 RColorBrewer_1.0-5 bitops_1.0-6  caTools_1.16 colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4  gdata_2.13.2 gtable_0.1.2 gtools_3.2.1 labeling_0.2  munsell_0.4.2 proto_0.3-10 reshape2_1.2.2 scales_0.2.3  stringr_0.6.2
I've seen in many other posts suggestions to manually run the BQSR.R script on the data, but I don't have a CSV file yet, and there were no instructions on how to manually run BQSR.R, i.e., what arguments to specify to the Rscript command, and in what order.
Any help solving this problem would be greatly appreciated.