Does GATK SetNmMdAndUqTags reduces the size of a CRAM?
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9 months ago
Sd • 0

I performed GATK SetNmMdAndUqTags on a CRAM file for Whole Genome Sequencing after completing the MarkDuplicates step. The initial size of the CRAM file was 19GB, and after performing the SetNmMdAndUqTags operation, its size reduced to 8GB. The following is the log file I obtained after completing the SetNmMdAndUqTags step. I am unsure whether it executed successfully or not. Can someone help me with this?

> [Tue Oct 17 22:13:26 EDT 2023] picard.sam.SetNmMdAndUqTags done. Elapsed time: 164.26 minutes.
Runtime.totalMemory()=2516582400
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
java.lang.ArrayIndexOutOfBoundsException: Index 90338345 out of bounds for length 90338345
        at htsjdk.samtools.util.SequenceUtil.sumQualitiesOfMismatches(SequenceUtil.java:568)
        at picard.sam.AbstractAlignmentMerger.fixUq(AbstractAlignmentMerger.java:629)
        at picard.sam.AbstractAlignmentMerger.fixNmMdAndUq(AbstractAlignmentMerger.java:615)
        at picard.sam.SetNmMdAndUqTags.fixRecord(SetNmMdAndUqTags.java:147)
        at picard.sam.SetNmMdAndUqTags.lambda$doWork$0(SetNmMdAndUqTags.java:135)
        at java.base/java.util.stream.ReferencePipeline$15$1.accept(ReferencePipeline.java:540)
        at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
        at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)
        at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
        at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
        at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
        at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
        at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596)
        at picard.sam.SetNmMdAndUqTags.doWork(SetNmMdAndUqTags.java:136)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289)
        at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)
CRAM WGS sam GATK SetNmMdAndUqTags • 350 views
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No theres's an error.

this error happens when the END position of the read is greater than the chromosome. https://github.com/samtools/htsjdk/blob/3964abef798ed1db46321fc9c23827dbede44e1b/src/main/java/htsjdk/samtools/util/SequenceUtil.java#L568

how did you map the reads ? check the BAM with https://gatk.broadinstitute.org/hc/en-us/articles/360036854731-ValidateSamFile-Picard-

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