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  • Read Group

    Hello,

    Does anybody know the definition of read group?

    I checked Sam format specification and there is no definition.

    We have 8 lanes of whole exome data (1 sample/ lane) from an Illumina run, are all these lanes one read group? Or is each lane a separate read group? Also, can each lane have more than one read group?

    Thanks!

  • #2
    Originally posted by comorado View Post
    Hello,

    Does anybody know the definition of read group?

    I checked Sam format specification and there is no definition.

    We have 8 lanes of whole exome data (1 sample/ lane) from an Illumina run, are all these lanes one read group? Or is each lane a separate read group? Also, can each lane have more than one read group?

    Thanks!
    Each lane is it's own read group. See section 2.1 "Header section" for more details (it is in the specification).

    Comment


    • #3
      Thanks Nilshomer, for your prompt reply. For me it was not obvious after reading the Sam specification that each line is from one read group . Thanks a lot again.

      Comment


      • #4
        Originally posted by comorado View Post
        Thanks Nilshomer, for your prompt reply. For me it was not obvious after reading the Sam specification that each line is from one read group . Thanks a lot again.
        You mean each lane, not each line

        Use the "PU" attribute in the read group to indicate which lane:
        Code:
        Platform unit (e.g. lane for Illumina or slide for SOLiD); should be a full, unambiguous identifier

        Comment

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