the meaning of CIGAR column in SAM file outputs by BWA

[holywoool]

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!

[Bruins]

Hi,

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

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

Cheers

[holywoool]

Well,the following link gives answers!

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002/figure/F1/