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Old 01-03-2011, 10:11 PM   #1
holywoool
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Arrow 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:
Quote:
S Soft clip on the read (clipped sequence present in <seq>)
Quote:
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!
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Old 01-03-2011, 11:50 PM   #2
Bruins
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Hi,

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

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

Cheers
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Old 01-04-2011, 04:34 AM   #3
holywoool
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Well,the following link gives answers!
http://www.ncbi.nlm.nih.gov/pmc/arti...002/figure/F1/
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