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  • the meaning of CIGAR column in SAM file outputs by BWA

    I used BWA to map 454 reads and the outputs were in SAM format.The sixth column is CIGAR which shows matching(M)/insertion(I)/deletion(D).However,there are another two operations which I don't understand their meanings:
    S Soft clip on the read (clipped sequence present in <seq>)
    H Hard clip on the read (clipped sequence NOT present in <seq>)
    What do Soft clip and Hard clip mean?Do they clip reads before mapping? and what's the difference between them?
    For example,I get one CIGAR as:
    4S20M1D20M15S
    how to explain 4S and 15S?
    Thank you!

  • #2
    Hi,

    I once wondered about this too, and got a very helpful explanation.

    http://seqanswers.com/forums/showthread.php?t=4882

    Cheers

    Comment


    • #3
      Well,the following link gives answers!
      http://www.ncbi.nlm.nih.gov/pmc/arti...002/figure/F1/

      Comment

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