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  • GATK BaseRecalibrator error message

    Hi all,
    I am trying to run the BaseRecalibrator in GATK but got an error message of:

    MESSAGE: SAM/BAM file SAMFileReader{test.sorted.bam} is malformed: The input .bam file contains reads with no platform information. First observed at read with name = 552_2035_733_F

    I am assuming that this is telling me that I need the platform information to be contained in the read group (SOLiD sequencing in this case). I was under the impression that it is not necessary to have this information in the file, or am I mistaken by this? Should having this information really matter? Or am I missing some flag that should be added that will skip this.
    Thanks

  • #2
    Platform information is indeed required by GATK.

    Since you're working with SOLiD data, be sure to have a look at the solid-specific arguments of the BaseRecalibrator.

    Comment


    • #3
      Hi,

      I am getting the same error:
      ERROR MESSAGE: SAM/BAM file SAMFileReader{*.bam} is malformed: The input .bam file contains reads with no platform information. First observed at read with name = HWI-ST565:24119R1ACXX:1:2106:16117:83155

      This is illumina. How can I circumvent this error?

      ~Thanks!

      Comment


      • #4
        You'll need to add the platform information to your read groups. You can use Picard tools' AddOrReplaceReadGroups (http://picard.sourceforge.net/comman...laceReadGroups) to reset the read group info.

        Comment


        • #5
          Hi All

          I am getting error in BaseRecalibrator step. I am using this command

          java -Xmx8g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R file.fa -I file_relgn.bam -knownSites snv.sorted.vcf -knownSites indels_sort.vcf -o file_recal.grp -plots file_recal.grp.pdf

          I am getting error like this

          ##### ERROR MESSAGE: Argument with name 'plots' isn't defined.

          Any help will be appreciated.
          Thanks in advance

          Comment


          • #6


            There doesn't seem to be an option to produce a plot from BaseRecalibrator. What are you trying to plot?

            Comment


            • #7
              I am trying to plot the graph before and after the baserecalibration.
              here is the doc

              Comment


              • #8
                The 'empirical - reported quality' plots e.g. page 5? In the recal.grp file the data is available for this (RecalTable2, cols 2, 6) it should be trivial to plot in R.

                Comment


                • #9
                  Originally posted by amitbik View Post
                  Hi All

                  I am getting error in BaseRecalibrator step. I am using this command

                  java -Xmx8g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R file.fa -I file_relgn.bam -knownSites snv.sorted.vcf -knownSites indels_sort.vcf -o file_recal.grp -plots file_recal.grp.pdf

                  I am getting error like this

                  ##### ERROR MESSAGE: Argument with name 'plots' isn't defined.

                  Any help will be appreciated.
                  Thanks in advance
                  It's a "new" tool.

                  Comment


                  • #10
                    Thanks a lot bruce01 and Zaag

                    I think there is some problem in Rscript thats why it is showing error.
                    I did as mentioned in the link



                    But again i am getting error

                    ##### ERROR MESSAGE: RScript exited with 1.

                    Comment


                    • #11
                      Do you have ggplot2 (Rlibrary)?

                      Comment

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