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  • keebs42
    Member
    • May 2009
    • 17

    #1

    sam/bam header lines

    Could someone point me to a description of the @SQ and @RG header lines? As in:
    @HD VN:1.0 GO:none SO:coordinate
    @SQ SN:1 LN:247249719
    @SQ SN:2 LN:242951149
    @SQ SN:3 LN:199501827
    @SQ SN:4 LN:191273063
    ...
    @RG ID:SRR001176 PL:ILLUMINA PU:BI.080220_SL-XAM_0002_FC20B2TAAXX.7 LB:Solexa-3628 PI:SM:NA12891 CN:BI
    @RG ID:SRR001180 PL:ILLUMINA PU:BI.080222_SL-XAT_0001_FC13355AAXX.7 LB:Solexa-3628 PI:610 SM:NA12891 CN:BI

    Most are straight forward, but I'm wondering specifically about @SQ SN: LN: and @RG PU:

    Thanks!
  • nilshomer
    Nils Homer
    • Nov 2008
    • 1283

    #2
    Originally posted by keebs42 View Post
    Could someone point me to a description of the @SQ and @RG header lines? As in:
    @HD VN:1.0 GO:none SO:coordinate
    @SQ SN:1 LN:247249719
    @SQ SN:2 LN:242951149
    @SQ SN:3 LN:199501827
    @SQ SN:4 LN:191273063
    ...
    @RG ID:SRR001176 PL:ILLUMINA PU:BI.080220_SL-XAM_0002_FC20B2TAAXX.7 LB:Solexa-3628 PI:SM:NA12891 CN:BI
    @RG ID:SRR001180 PL:ILLUMINA PU:BI.080222_SL-XAT_0001_FC13355AAXX.7 LB:Solexa-3628 PI:610 SM:NA12891 CN:BI

    Most are straight forward, but I'm wondering specifically about @SQ SN: LN: and @RG PU:

    Thanks!
    See the SAM format on the SAMtools website.

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