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Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Does GATK BaseRecalibrator work with solid Lifescope Bam files?

Does GATK BaseRecalibrator work with Bam files produces with the SOLID Lifescope mapper?

You show in the a base quality recalibration presentation that recalibration also should work on SOLID data. But you don't mention if it also works for Bam files produced with lifescope. BWA mapping quality is from 0-37 , Lifescope mapping quality is from 0 - 95.

I get an ArrayIndexOutOfBoundsException on the lifescope Bam files.

`##### ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: -92
at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(
at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(
at org.broadinstitute.sting.utils.baq.BAQ.baqRead(
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.gatk.CommandLineGATK.main(

ERROR ----------------------------------------------`

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    The error you're getting is unrelated to its origin, it's due to a bug that is fixed in the latest version of GATK. Just upgrade your version and it will work fine.

  • The version I am using is
    The Genome Analysis Toolkit (GATK) v2.3-9-ge5ebf34, Compiled 2013/01/11 22:43:14

    which is fairly recent. So there is already a newer 2.3.9 build online? Or will it be fixed in 2.4?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Oh that's weird, that is our latest version. Let me check if the fix is still pending.

  • Ok I am interested in the answer. To check for other problems I also ran Picard validate bam.
    I get a lot of NM tag missing errors:

    WARNING: Record 1, Read name 1212_1948_428, NM tag (nucleotide differences) is missing

    And just some mate related errors:

    ERROR: Record 20985168, Read name 164_312_583, Mate alignment does not match alignment start of mate
    ERROR: Record 20985168, Read name 164_312_583, Mate negative strand flag does not match read negative strand flag of mat

  • LisaLattaruloLisaLattarulo San Diego, CAMember

    Hi - quick follow up @WimS. Did you ever figure out what do do with the all WARNING: ....NM tag (nucleotide differences) is missing? Did you have to fix these or did they run through anyhow? If you did fix them, how did you? I am currently running into this issue and haven't been able to find resolution yet. Thank you!!

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