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Created 2015-10-23 17:40:36 | Updated 2015-10-23 17:42:20 | Tags: baserecalibrator iontorrent error

Comments (3)


I'm doing pre-processing in Ion Torrent samples. But I'm getting an error while running BaseRecalibrator.

Here are the steps I followed:

  1. Sort BAMs
  2. Add or change RG from Picard tools
  3. Indel Realignment from GATK
  4. Base recalibration from GATK [ERROR]

This is the error I get:

ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.ClassCastException: [I cannot be cast to [B
        at org.broadinstitute.gatk.engine.recalibration.RecalUtils.isColorSpaceConsistent(RecalUtils.java:888)
        at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.badSolidOffset(BaseRecalibrator.java:308)
        at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.calculateSkipArray(BaseRecalibrator.java:302)
        at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:267)
        at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:136)
        at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228)
        at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216)
        at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
        at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
        at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102)
        at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
        at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108)
        at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
        at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
        at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.4-46-gbc02625):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: [I cannot be cast to [B

Here is the code I have used: java -XX:ParallelGCThreads=4 -Xmx4G -jar $GATK_HOME/GenomeAnalysisTK.jar -R $REF -T BaseRecalibrator -I $FILE -knownSites $KNOWN_SITES -o $BAMs/BaseRecalibration/$SAMPLE.recal.table

Does anyone know how to fix this?

Created 2014-11-07 08:45:55 | Updated | Tags: indels iontorrent hardfiltration

Comments (1)


I'm having the following problem: I am working with different sequencing datasets (Ion Torrent) resulting from targeted sequencing. As it is not the full exome, I have to use hard filtration to filter those SNPs and indels (detected by the Haplotype Caller) that seem to be reliable. Regarding the SNPs the results are quite satisfying. However, regarding the indels, I have a relatively long list of possible candidates. Unfortunately I don't know the biological truth, so it is very hard to adjust certain parameters to finally exclude those indels, which are false positives.

Therefore, I was thinking of a dataset, resulting from sequencing with Ion Torrent, and a list with validated indels in this dataset. With this dataset it would be possible to optimize my pipeline for detecting the true indels, and not all those false positives.

As you propose certain thresholds for the hard filtration of indels, I thought you might have some datasets with validated indels, on which your proposals rely?! If so, is there a place where I can find those datasets?

Many thanks in advance for your help!

Created 2013-05-02 19:53:14 | Updated | Tags: iontorrent

Comments (13)

Recent thread: http://gatkforums.broadinstitute.org/discussion/1677/best-practice-for-variant-calling-on-ion-torrent-data-with-gatk

Any progress on some Best Practices for data processing pipelines for variant detection with GATK on Iontorrent PGM/Proton data?

Any plans for GATK branches to deal with the particulars of IonTorrent output?

Created 2012-12-20 21:47:53 | Updated 2012-12-21 16:34:27 | Tags: combinevariants vcf iontorrent

Comments (1)

I am trying to merge two vcfs (SNVs and INDELs) from the same sample. The problem appears to be that the INDEL vcf defines "combined_sample_name" but the SNV vcf does not. So when I merge I get two sample columns. How can I force GATK to treat them as a single sample?

I tried --assumeIdenticalSamples to do a "simple merge," but that made no difference.

As a side note, these vcfs are from an Ion Torrent machine.


java -jar $GATK \
    -T CombineVariants \
    --assumeIdenticalSamples \
    -V:${baseFolderName} ${i}/SNP_variants.vcf \
    -V:${baseFolderName} ${i}/indel_variants.vcf \
    -o ${RESULTS_DIR}/${baseFolderName}_variants.vcf

Created 2012-10-16 14:35:13 | Updated 2012-10-16 21:22:21 | Tags: best-practices iontorrent

Comments (6)


I wonder how well GATK works with Ion Torrent data. Is there any recommended practice to handle Ion Torrent data, especially SNP and indel calling, with GATK?

Thanks, XZ