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  • Zaag
    replied
    Do you have ggplot2 (Rlibrary)?

    Leave a comment:


  • amitbik
    replied
    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.

    Leave a comment:


  • Zaag
    replied
    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.

    Leave a comment:


  • bruce01
    replied
    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.

    Leave a comment:


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

    Leave a comment:


  • bruce01
    replied


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

    Leave a comment:


  • amitbik
    replied
    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

    Leave a comment:


  • vdauwera
    replied
    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.

    Leave a comment:


  • rpauly
    replied
    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!

    Leave a comment:


  • vdauwera
    replied
    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.

    Leave a comment:


  • lre1234
    started a topic GATK BaseRecalibrator error message

    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

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