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  • Errors from Picard and GATK on a BWA paired-end BAM

    I have two samples with the following errors. One had an error in Picard MarkDuplicates. The other in GATK IndelRealigner. Both samples were mapped using BWA on paired-end data.

    Does anyone know of a way to resolve these errors without removing reads from the sample? Any input at all is greatly appreciated

    In Picard:


    Code:
    Exception in thread "main" net.sf.picard.PicardException: Value was put into PairInfoMap more than once.  2: foo:USI-EAS034_4_PE1_FC304CLAAXX:2:22:534:490
    	at net.sf.picard.sam.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:124)
    	at net.sf.picard.sam.CoordinateSortedPairInfoMap.remove(CoordinateSortedPairInfoMap.java:78)
    	at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:61)
    	at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:294)
    	at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:117)
    	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
    	at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:101)
    and in GATK:

    Code:
    ##### ERROR MESSAGE: Exception when processing alignment for BAM index USI-EAS034_2_PE_FC307TBAAXX:3:79:1633:1917 2/2 45b aligned read.

  • #2
    It would probably help if you showed all the .sam entries for reads with that name.

    Comment


    • #3
      I am searching for them, but these BAMs are quite large and it will require some time. In the meantime, do you have any thoughts on the problems?

      Comment

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