Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
BaseRecalibrator: only the original data is plotted
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?