I finally managed to install gsalib and so I checked the plots coming out of the BaseRecalibrator runs I was running. Then I noticed that the plots had only the original data in it, and not the recalibrated data.
More details on my setup:
Ran BaseRecalibrator as follows
java -Xmx32G -jar /path/to/GenomeAnalysisTK.jar -R /path/to/ucsc.hg19.fasta \
-L /path/to/my/regions.bed -I joined_file.bam -knownSites \
/path/to/dbsnp.vcf -o joined_file.grp -nct 24 --plot_pdf_file result.pdf
Results are similar to the attached file.
Any idea on what I could be doing wrong?