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  • understanding dwgsim_eval output

    Here is the command line:

    Code:
    dwgsim_eval -b -g 0 1300000.bwa.01.sorted.bam
    Here is the first line of the output:
    Code:
    60           13 / 2111834                 13       2111834       2600004  6.156e-06  6.156e-06  5.000e-06  5.000e-06
    There were 1300002 pairs so a total of 2600004. I read what information was on the dwgsim website, but I am still having trouble understanding how to read this output. Any help/comments/input at all would be greatly appreciated.

  • #2
    I would be happy to explain given specific questions, and then update the documentation: http://sourceforge.net/apps/mediawik..._-_dwgsim_eval

    Comment


    • #3
      Thanks, and for starters does the 13 / 2111834 indicate that 13 out of 2111834 reads mapped correctly at that threshold? The second column ('mc' on the documentation) indicates this, correct?

      Comment


      • #4
        Could you print the line in question?

        Comment


        • #5
          Code:
          60           13 / 2111834                 13       2111834       2600004  6.156e-06  6.156e-06  5.000e-06  5.000e-06
          Here is the line in question from my output.
          The only thing that I understand for sure is that 60 in the first column is the minimum mapping quality threshold. The documentation indicates 19 columns in the output, whereas I have only 9. Maybe some columns are showing null values?

          This might be asking a bit much, but could you tell me the meanings of '13/2111834' , '13' , '2111834', and '2600004'? Perhaps that could help me understand what is happening here.

          Again, i used parameters '-g 0' and '-b' for BWA.
          Last edited by oiiio; 08-15-2011, 01:25 PM. Reason: more details

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          • #6
            I think you have an old version. I released a dwgsim package update yesterday.

            Nils

            Comment


            • #7
              Code:
              In function "process_bam": Warning[OutOfRange]. Variable/Value: 2L 17664817 17664105 1 0 4 0 0 2 0 0 116ac.
              Message: [dwgsim_eval] read was not generated by dwgsim?.
              Does the new version of dwgsim_eval require that reads were generated by the newer version of dwgsim ?

              Comment


              • #8
                Yes it does unfortunately. Those two are intimately paired. Also, you can subscribe to [email protected] to get notified with updates.

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                • #9
                  Are there any errors in the old versions of dwgsim and _eval? I wanted to verify results from my own BAM parser that I am using on dwgsim data.

                  If possible do you think you could help me understand what I am seeing in my output from the old version?

                  Comment


                  • #10
                    Sure, could you give me the version #? You might be able to get it when you run dwgsim without any options.

                    Comment


                    • #11
                      The version is 0.1.2

                      Comment


                      • #12
                        Caveat: I really like the new version a lot better, and there may be bugs in the old version. Below are the columns:
                        #1: metric
                        #2: # mapped correctly at the threshold
                        #3: # of mapped at the threshold
                        #4: # mapped correctly at or greater than the threshold
                        #5: # of mapped at or greater than the threshold
                        #6: # of reads total
                        #7: fraction of reads mapped correctly of those mapped, at the threshold
                        #8: fraction of reads mapped correctly of those mapped, at or greater than the threshold
                        #9: fraction of reads mapped correctly out of all reads, at the threshold
                        #10: fraction of reads mapped correctly out of all reads, at or greater than the threshold

                        Comment


                        • #13
                          Awesome, thanks. I will upgrade to the newer version, but for now I have a ton of data that was generated with my older one.

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