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  • GATK IndelRealigner error

    I have problems with the GATK IndelRealigner. I run GATK version 1.0.5365

    Except the standard input and output files I use:
    -compress 0
    -L chr_number
    -B:indels,VCF dbSNP_indelfile.vcf

    The pipeline I use look like this:
    1. Split fastq-files into smaller parts (paired-end)
    2. Align each parts with BWA
    3. sort each part with samtools
    4. merge with samtools
    5. run GATK -T IndelRealigner on each chromosome (after RealignerTargetCreator of course)

    All chromosomes except number 11 is going ok.

    In chr11 I get this error:
    java.lang.IllegalArgumentException: Alignments added out of order in SAMFileWriterImpl.addAlignment for /glob/jonasc/alignment_test2/pipe_line_test_sorted_realign.bwa.11.bam. Sort order is coordinate. Offending records are at [11:51571970] and [11:51571888]

    Using samtools view on the region in the input bam-file I can see that the reads are sorted.

    Any help to solve this would be useful.

  • #2
    Get some satisfaction: http://getsatisfaction.com/gsa

    Comment

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