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Problem with BaseRecalibrator in v2.2-8-gec077cd

Hello dear GATK People,
I'm failing with BaseRecalibrator from the new GATK version - my pipeline worked with the 2.1-11, below is my error message.
Any quick fix or should I stick to the old version?
Ania
ERROR stack trace
java.lang.IllegalArgumentException: fromIndex(402) > toIndex(101)
at java.util.Arrays.rangeCheck(Unknown Source)
at java.util.Arrays.fill(Unknown Source)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateKnownSites(BaseRecalibrator.java:280)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateSkipArray(BaseRecalibrator.java:259)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:239)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:287)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:252)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.2-8-gec077cd):
.....
Answers
Hi there, this could be a bug -- could you please check that your BAM file passes validation (with validateSAMFile) and if it does, try to narrow this down as much as possible to a small set of reads + known sites that triggers the error, and then send us the snippets for testing?
Hi Geraldine,
so the input file validates with picard, it also works with the walker from GATK 2.1-11. I can see that the offensive reads are in several places, as after removing the first problematic region it continues through the rest of the chromosome, but fails on the next one.
The alignement is mRNAseq against mm10, done with Tophat. Might it be that introns are the issue here? For the attached file I'm getting
Hi there,
I think I've fixed this issue for you. The fix should be available in a few hours when version 2.2-9 is released.
Hi everyone,
I'm facing a similar issue with GATK v4.1.0.0 (HTSJDK v2.18.2 and Picard v2.18.25). I'm using GATK Docker image broadinstitute/gatk:4.1.0.0.
Following what I read here, I checked the bam file and everything seems fine:
gatk ValidateSamFile --INPUT sorted.bam --MODE SUMMARY
But when run BaseRecalibrator got the fromIndex toIndex error:
gatk BaseRecalibrator --input sorted.bam --output sorted.baserecalibrator_report.txt --reference GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.fasta --use-original-qualities true --known-sites snp151common_tablebrowser.bed.bgz --known-sites snp151flagged_tablebrowser.bed.bgz
I downsampled the fastq files and got similar results.
However, when giving only the reduced known-sites file (
--known-sites snp151flagged_tablebrowser.bed.bgz
) and specifying two intervals (--intervals chr22 --intervals chrY
), it worked.I attached the downsampled bam file and the reduced known-sites file, and the reference file can be found here.
I hope you can help me understanding what is going on and how to fix it.
Thank you in advance.
Best regards,
Miguel
Issue · Github
by bhanuGandham
Hi @mpmachado
I have created a bug report for this issue on github. Here is link for it: https://github.com/broadinstitute/gatk/issues/5807
You can follow the progress for this issue there and you could also post in that issue ticket for more information.