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Old 06-14-2010, 11:01 AM   #1
Location: Europe

Join Date: Apr 2010
Posts: 46
Default SAM Format - Hard Clip


I was wondering can shed light on the following question on the hard-clipping within the SAM format (I'm not able to pinpoint an answer in the spec):

If a query read aligns with H's on either end (i.e. hard-clipped), I understand the query sequence itself is truncated in the SEQ field.

My question is - in these cases, should the POS reflect
(a) the index of the first aligned base in the reference, or b
(b) the index of the first base in the reference correspond to the first H.

Thanks for your time.
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