BaseRecalibrator: only the original data is plotted
Posted in Ask the GATK team | Last updated on 2013-04-30 15:11:39

Comments (6)


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 on the two sample BAM
  • In all cases used -L to limit to the regions of interest

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?

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