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  • read group: GATK or BWA option?

    Hi NGS users,
    when I run GATK recalibration score, it returns me the error about read group:

    SAM/BAM file SAMFileReader{/dati1/Analysis_NGS/prova_s8/prova_GATK_localrealignment.bam.sorted.bam} is malformed: The input .bam file contains reads with no read group.

    So I try to use the option with a random string and the program runs:

    --default_platform Illumina --default_read_group HWUSI-EAS703

    I don't know if this is correct or if I have to rerun bwa, using the patch and use this options:

    -i read group identifier (ID)
    -m read group sample (SM), required if ID is given
    -l read group library (LB)
    -p read group platform (PL)

    Any suggestions?
    Thanx a lot,
    ME

  • #2
    Hi,

    I had this issue, and after patching bwa to the lastest update I run my sampe with

    -r STR read group header line such as `@RG\tID:foo\tSM:bar' [null]

    I specify ID, SM, LB and PL. So far no trouble with GATK on the downstream files.

    Comment


    • #3
      It depends!

      If you have one lane/group, using the GATK default_read_group is as good as using the patched bwa.
      But if you are analyzing multiple lanes/groups, patched bwa should be used. The GATK recalibration requires different group name in order to analyze each group seperately and default_read_group only assign one default group name to all reads. This can affect the GATK recalibration score.

      .

      Comment


      • #4
        malformated @RG line

        Hi NGSer,
        i run into the problem that my Readgroup Header is not accepted by bwa and i dont know why

        heres my code:

        Code:
        bwa sampe -r @RG ID:ILLUMINA-52179E_0039_FC62HDBAAXX_1_1 SM:48_2 PL:illunmina ./testingscripts/chrY.fa ./testingscripts/48_2_1_KESC1_mymod.sai./testingscripts/48_2_2_KESC1_mymod.sai ./testingscripts/48_2_1_KESC1_mymod.fastq ./testingscripts/48_2_2_KESC1_mymod.fastq > ./testingscripts/chrYvs48_2_1_KESC1_mymod_48_2_2_KESC1_mymod.sam
        any help would be nice . I also tested with \t explicit between the tags but with no success , thx in advance Aicen

        Comment


        • #5
          you should separate the tags by tabulators instead of whitespaces just put \t between the tags
          like:
          Code:
          bwa sampe -r "@RG\tID:ILLUMINA-52179E_0039_FC62HDBAAXX_1_1\tSM:48_2\tPL:illumina" ./testingscripts/chrY.fa ./testingscripts/48_2_1_KESC1_mymod.sai./testingscripts/48_2_2_KESC1_mymod.sai ./testingscripts/48_2_1_KESC1_mymod.fastq ./testingscripts/48_2_2_KESC1_mymod.fastq > ./testingscripts/chrYvs48_2_1_KESC1_mymod_48_2_2_KESC1_mymod.sam
          Last edited by ulz_peter; 10-18-2011, 02:25 AM. Reason: forgot one tab

          Comment


          • #6
            " - this missed

            my string missed the " at start and end and i needed to write \\t in my script so that the command lane statement went right, thx for your help

            Comment


            • #7
              With BWA output, I usually use Picard's AddOrRemoveReadGroups.jar before feeding the BAM file to GATK. You can provide all the necessary read group details to ensure GATK works.

              Comment


              • #8
                bwa

                Well, at the moment it seems to work fine, did u make other experience where bwa's -r opton could fail ? Because i dont want to draw the short stick at the end of the work realising sth. didnt work with the RG header^^ .

                Iam using GATk for further variant calling btw
                Last edited by Aicen; 10-18-2011, 10:52 AM.

                Comment


                • #9
                  To have a bam that can be used in GATK, use this RG header (note the "\t")

                  bwa sampe -r @RG"\t"ID:SAMPLE1_RG1"\t"PL:illumina"\t"PU:SAMPLE1_RG1_UNIT1"\t"LB:SAMPLE1_LIB1"\t"SM:SAMPLE1

                  Comment


                  • #10
                    Originally posted by ulz_peter View Post
                    you should separate the tags by tabulators instead of whitespaces just put \t between the tags
                    like:
                    Code:
                    bwa sampe -r "@RG\tID:ILLUMINA-52179E_0039_FC62HDBAAXX_1_1\tSM:48_2\tPL:illumina" ./testingscripts/chrY.fa ./testingscripts/48_2_1_KESC1_mymod.sai./testingscripts/48_2_2_KESC1_mymod.sai ./testingscripts/48_2_1_KESC1_mymod.fastq ./testingscripts/48_2_2_KESC1_mymod.fastq > ./testingscripts/chrYvs48_2_1_KESC1_mymod_48_2_2_KESC1_mymod.sam
                    Hello ulz_peter,

                    I tried writing code according to you , But didnt get success.

                    @HWI-ST741:204: D0TEJACXX:8:1101:1107:1901 1:N:0: BC=ACGTAA SAMPLE=1 LENGTH=64 MEAN_QUAL=38.6

                    Here is my sample Can you please help me writing the code for this sample.

                    Thanking in anticipation.

                    Comment

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