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  • thedamian
    replied
    Yes, I've already realised how to do this. Another option is to use Picard's AddOrReplaceReadGropus.jar.
    Code:
    java -jar AddOrReplaceReadGroups I=my.bam O=myGr.bam LB=whatever PL=illumina PU=whatever SM=whatever
    Of course prior using AddOrReplaceReadGroups your .sam file needs to pass Picard's validation (ValidateSamFile.jar)

    Leave a comment:


  • colinmolter
    replied
    hi the damian,
    when creating your sam file, you have to add read group header.
    this should work:

    bwa samse -r @RG\tID:IDa\tSM:SM\tPL:Illumina ref.fa my.sai my.fastq > my.sam
    bests

    colin

    Leave a comment:


  • thedamian
    replied
    Hi, I have the same problem as Hiroki.

    I made a sam file using command:
    Code:
    bwa samse ref.fa my.sai my.fastq > my.sam
    then, I have creaded .bam file:
    Code:
    samtools view -bS my.sam > my.bam
    next, I have sorted my.bam file:
    Code:
    samtools sort my.bam my_sorted
    Using GATK, I need to put a .bam file as an input.
    According to the instructions from http://www.broadinstitute.org/gsa/wi...s_for_the_GATK I have used Picard's ReordereSam, to reorder reads:
    Code:
    java -jar ReordereSam.jar I=/path/my_sorted.bam O=/path/my_reordered.bam R=/path/ref.fa
    Trying i.e.
    Code:
    java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R /paht/ref.fa -I /path/aln_reordered.bam
    an error is returned:
    HTML Code:
    ##### ERROR MESSAGE: SAM/BAM file /path/my_reordered.bam is malformed: SAM file doesn't have any read groups defined in the header.  The GATK no longer supports SAM files without read groups
    I have tried Picards AddOrReplaceReadGroups.jar and ReplaceSamHeader.jar but it didn't help me.

    Any suggestions how to bulid proper .bam file for GATK?
    thx

    Leave a comment:


  • desaila
    replied
    I've run into similar issues using GATK for bam files, and Picard. The option that always has helped me when I knew hte BAM file was "ok,"

    java [args to jvm] GATK.jar [GAKT opts] VALIDATION_STRINGENCY=SILENT

    Leave a comment:


  • Hiroki
    replied
    Thanks ulz_peter!

    I was told to use Picard from another guy.
    Now I'm trying it.

    Thank you so much anyways!

    Leave a comment:


  • ulz_peter
    replied
    you could easily change the header using samtools, but that won't solve the problem as the readgroup is necessary in each alignment section as well.
    You could have a look in the AddOrReplaceReadGroup Utility of Picard:
    http://picard.sourceforge.net/comman...laceReadGroups

    I don't know if that changes the header as well but if not have a look here:
    http://picard.sourceforge.net/comman...placeSamHeader

    Leave a comment:


  • Hiroki
    started a topic Changing header of BAM

    Changing header of BAM

    Hello,

    I apologize if my question is redundant....

    I created bam files from fastq files by ELAND_standalone and tried to feed them to GATK. Then I got the following error message.
    ##### ERROR MESSAGE: SAM/BAM file reanalysis.bam is malformed: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups
    ##### ERROR -

    How can I change the header? Samtools?

    Thank you very much.

    Hiroki

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