The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

#### ☞ Did you remember to?

1. Search using the upper-right search box, e.g. using the error message.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

#### ☞ Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks (  ) each to make a code block as demonstrated here.

GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

# BaseRecalibrator: only the original data is plotted

Member
edited April 2013

Hello,

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?

Tagged:

• Member

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.

• Member

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

Thanks

• Member

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://github.com/broadgsa/gatk.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`

• Member

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? And...how long are your reads? Did you use bwa-mem to align? Thanks!!