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Does GATK BaseRecalibrator work with solid Lifescope Bam files?

WimSWimS Posts: 25Member

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(BAQ.java:158)
at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:225)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530)
at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243)
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:248)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219)
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:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

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

Answers

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