It looks like you're new here. If you want to get involved, click one of these buttons!
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:
small Ion Torrent sequencing dataset (~50 genes), approximately 500 Mb per sample
realigned indels of matched samples together -> produced a single BAM
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?