Markduplicate error on gatk4

Dear All . I use samtools (1.6) for merge bam file and then I run markduplicate. I have this error:

Exception in thread "main" htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 1: 432_L002:B0P8DQ1:88:CA2D7ACXX:2:2314:7568:79248

I use this command:

picard MarkDuplicates I=mapped_reads/bam/432_sortedR.bam O=mapped_reads/merged_samples/432.dedup.bam M=mapped_reads/merged_samples/432.dup.metrics.txt REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT
Any idea how to resolve? with markduplicate from gatk3.8 I don't have this errror

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Answers

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Do you merge mapped bam files or do you merge an unmapped bam file and a mapped bam file?

    If you are doing the former MarkDuplicates can merge files for you. Just indicate multiple bam files in the command as I= and give one O= output. All files will be merged at the end.

    If you are doing the latter then you need to use PICARD MergeBamAlignment for that.

  • mauriziopolanomauriziopolano udineMember

    @SkyWarrior thanks so much!! I merged bam files before of markduplicate step using samtools 1.6 merge and I merge the complete alignment from bwa .

  • mauriziopolanomauriziopolano udineMember
    edited April 2018

    I try to use Markduplicate fr createe unique bam . However I have the same error

    [Wed Apr 04 13:20:19 UTC 2018] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.03 minutes.
    Runtime.totalMemory()=910688256
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    Exception in thread "main" htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once.  1: 432_L001:B0P8DQ1:88:CA2D7ACXX:1:1303:8853:70577
        at htsjdk.samtools.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:133)
    
  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
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