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BaseRecalibrator: only the original data is plotted

luca_beltrameluca_beltrame Member Posts: 10
edited April 2013 in Ask the GATK team


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?

1452 x 594 - 78K

Best Answer


  • luca_beltrameluca_beltrame Member Posts: 10

    Well, it turned out that BaseRecalibrator needs to be run twice. I found it thanks to the workshop material, as the documentation of the tools and the other places I looked at were extremely lacking.

  • MeenuMeenu Member Posts: 10

    HII luca beltrame

    Can you please let me know from where and how to install gsalib.
    Because i also have run Base-recalibration step that is creating plot .grp file but not creating plot pdf file.
    Please let me know how to generate plot pdf file


  • luca_beltrameluca_beltrame Member Posts: 10

    The instructions published elsewhere are needlessly complicated. You don't need ant, or anything of the sort. You will however need a working installation of R

    Check out the GATK sources:

    git clone git://

    Then navigate to the gatk/public/R/src/org/broadinstitute/sting/utils/R/ directory

    Instruct R to build the package:

    R CMD build gsalib/

    And you'll get a gsalib_1.0.tar.gz package in the directory. Then just install it with

    R CMD INSTALL gsalib_1.0.tar.gz

  • MartaMarta Member Posts: 12

    Dear Luca, I'm trying to analyze data from Ion Torrent (a dataset of 11 genes). I'm at the beginning of my analysis and I would like to be sure of my chooses. We used AmpliSeq for the enrichment. Did you? do you think that will be better to align against the whole genome or the BED file of my experimental disegn? long are your reads? Did you use bwa-mem to align? Thanks!!

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,985 admin

    Hi Marta,

    I would appreciate if you could please repost this as a new question. We would like to keep all discussions as coherent as possible, focused on a specific topic. The topic here is using gsalib for Base Recalibration, not the peculiarities of IonTorrent data. Tacking on new questions as comments in other discussions makes it difficult for other users later on to find relevant information. If you would like to ask a specific user for advice because you saw they have experience with the type of data you are using, you can mention them by name with an character in front (like this: @Marta) and they will receive a notification bringing your post to their attention.

    Geraldine Van der Auwera, PhD

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