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  • Maq output to SAM format

    1> I have been using MAQ for a while. Now I would like to move on the BWA. Is there any convinent method to convert a MAQ output (.map) to SAM format so to ease comparison between MAQ and BWA?

    2> Regarding the SAM format output by BWA, there is a <flag> column. I read from the manual that it's a bitwise flag. But in my BWA output I get numeric value, (e.g. 83, 99, 163, etc). How can I interpret the result?

    I would really appreciate your help.
    Marco

  • #2
    1. There is an excutable file "maq2sam" come with samtools package to allow you convert maq out to sam format.

    2. For FLAG field, if you want to parse it, simply use $FLAG & 0x01(02, 20, 20..) to determine the meaning of the FLAG bits.

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    • #3
      Originally posted by totalnew View Post
      2. For FLAG field, if you want to parse it, simply use $FLAG & 0x01(02, 20, 20..) to determine the meaning of the FLAG bits.
      The latest trunk version of samtools also has a "-X" flag to the "samtools view" command to display the flag using intelligible characters. I find this extremely useful.

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      • #4
        Originally posted by totalnew View Post
        1. There is an excutable file "maq2sam" come with samtools package to allow you convert maq out to sam format.

        2. For FLAG field, if you want to parse it, simply use $FLAG & 0x01(02, 20, 20..) to determine the meaning of the FLAG bits.
        Thank you totalnew. I have downloaded the samtools 0.1.5c. I think I will use the maq2sam-long for my 75bp long read.
        Marco

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        • #5
          Originally posted by nilshomer View Post
          The latest trunk version of samtools also has a "-X" flag to the "samtools view" command to display the flag using intelligible characters. I find this extremely useful.
          I cannot find the flag '-X' in samtools view. Am I using the old version?

          ps. I am using 0.1.5c
          Marco

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          • #6
            Originally posted by marcowanger View Post
            I cannot find the flag '-X' in samtools view. Am I using the old version?

            ps. I am using 0.1.5c
            Use the latest trunk version (via svn checkout). I think mine is r442.

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            • #7
              Originally posted by nilshomer View Post
              Use the latest trunk version (via svn checkout). I think mine is r442.
              I see. I am using the r385 so I think that's the reason.

              One more simple question, what type of quality score associated fastq file does BWA expects? I have searched in the manual but it just says fastq. I don't know if I should convert the my fastq file to sanger fastq first before proceeding.
              Marco

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              • #8
                Originally posted by marcowanger View Post
                I see. I am using the r385 so I think that's the reason.

                One more simple question, what type of quality score associated fastq file does BWA expects? I have searched in the manual but it just says fastq. I don't know if I should convert the my fastq file to sanger fastq first before proceeding.
                It would be Sanger FASTQ, since BWA is written by Heng Li (at Sanger).

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                • #9
                  Originally posted by marcowanger View Post
                  Thank you totalnew. I have downloaded the samtools 0.1.5c. I think I will use the maq2sam-long for my 75bp long read.
                  Yes, for 75bp read, you may have to use maq2sam-long, otherwise, otherwise you will get seg fault :<.

                  I have not downloaded new samtools, I guess it will be more handy to use samtools view -x. For quality score, nilshomer said the right, it is

                  $sanger_quality_char = chr($phred_quality + 33)
                  Last edited by totalnew; 08-10-2009, 08:22 AM.

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