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  • picard HSmetrics

    New to picard and trying to run HSmetrics on Ubuntu 12.0.4 using a BAM file. I am trying to get the predicted off-target reads. Thanks.

  • #2
    How to use the command: http://picard.sourceforge.net/comman...ulateHsMetrics

    Or is there an error that you have run into?

    Provide specifics for relevant help.

    Comment


    • #3
      picard HSmetrics

      So to run the command:

      Code:
      CalculateHsMetrics TARGET_INTERVALS=epilepsy.bam
      trying to calculate the predicted off-target reads on the Bed file I converted to a BAM using Bedtools. Is this BAM aligned if not how do I align it. I have the hg19 fasta or is there a better way? Thanks.

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      • #4
        One thing you need is a bed file of the target regions. Do you have this?

        Comment


        • #5
          picard HSmetrics

          Yes I do have a bed file of the targets and a bam file. I used the bedToBam tool in bedtools, but do not think it is aligned. Thanks.

          Comment


          • #6
            The .bam file is aligned, I think by definition. You can run the program with something like this:

            java -jar Tools/picard-tools-1.92/CalculateHsMetrics.jar BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/pathTohg19/hg19.fa

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            • #7
              picard

              Do the three files need to be in a folder and where do I put this folder? Do I cd into a directory? The picard-tools is in /usr/bin, but in order to see it I have to run ls /usr/bin. Also, is there a command to find out the version of picard-tools that is installed? Thanks

              Code:
              java -jar Tools/picard-tools-1.92/CalculateHsMetrics.jar BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/pathTohg19/hg19.fa

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              • #8
                You need to specify the correct path to all of the files. It does not matter if they are in the same directory. If you type /usr/bin/picard-tools and hit the tab button, it will fill out the version directory for you most likely.

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                • #9
                  picard HSmetrics

                  Code:
                    dnascopev@ubuntu:~/picardtools-1.72$ java -jar Tools/picard-tools-1.72/CalculateHsMetrics.jar BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt
                  Unable to access jarfile Tools/picard-tools-1.72/CalculateHsMetrics.jar. Thanks.

                  Comment


                  • #10
                    Don't use the code example posted by Heisman as is. It probably refers to a path that exists on Heisman's system. Do you actually have that directory on your machine?

                    I thought you had installed picard-tools from Ubuntu repository using "apt-get" yesterday.

                    Comment


                    • #11
                      picard HSmetrics

                      Yes I installed picard from apt-get. Thanks.

                      Comment


                      • #12
                        Picard tools from Ubuntu is an older version (i.e. v. 1.48 I think).

                        Give this command a try:

                        Code:
                        $ picard-tools CalculateHsMetrics BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt
                        If you get a file not found error then alternate version would be (assuming all these files are in the directory where you are running this command from)

                        Code:
                        $ picard-tools CalculateHsMetrics BI=./target_regions.bed TI=./target_regions.bed I=./epilepsy.bam O=./epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt

                        Comment


                        • #13
                          Yes, sorry, make sure you use paths relevant to you.

                          Comment


                          • #14
                            picard HSmetrics

                            Code:
                             picard-tools CalculateHsMetrics BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt
                            Code:
                             picard-tools CalculateHsMetrics BI=./target_regions.bed TI=./target_regions.bed I=./epilepsy.bam O=./epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt
                            ERROR: Unrecognized option: R

                            all three files are in the same directory (picardtools-1.72) Thank you.

                            Comment


                            • #15
                              Type "picard-tools CalculateHsMetrics", hit enter, and copy/paste the output here.

                              Comment

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