SAM Format - Hard Clip

Bio.X2Y · 06-14-2010, 11:01 AM

Hiya,

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.
Bio.

mrawlins · 06-14-2010, 11:34 AM

I don't recall having seen a SAM file with an H at the beginning of the CIGAR, only at the end. If the H is at the end (or somehow in the middle) then it shouldn't affect the position.

I would guess the position reflects the first base corresponding to the first H, though that may not be true. My reasoning is, if you're not starting from the first H, why even include the hard clipping in the first place? Since hard clipped sequence isn't included in the reported alignment, the only real reason for including it is to indicate the offset from the state position.

That being said, I'm just guessing here. If somebody knows conclusively, go with whatever they tell you.

Good Luck

Bio.X2Y · 06-14-2010, 11:45 AM

Thanks mrawlins! I'm leaning towards that interpretation too.

I'm trying to get a definitive stance since I'm in the process of writing some code that supports sam, and I'd prefer not to add another non-compliant application to the mix!

Anybody have something conclusive?
Thanks for your time

nilshomer · 06-14-2010, 11:49 AM

Quote:

Originally Posted by Bio.X2Y

Thanks mrawlins! I'm leaning towards that interpretation too.

I'm trying to get a definitive stance since I'm in the process of writing some code that supports sam, and I'd prefer not to add another non-compliant application to the mix!

Anybody have something conclusive?
Thanks for your time

Since the spec. is ambiguous in this case, and it probably should not be, could you send your email to the samtools help list (samtools-help@lists.sourceforge.net)? I think the spec. could benefit from this question.

lh3 · 06-14-2010, 12:04 PM

SAM spec: POS is "1-based leftmost POSition/coordinate of clipped sequence". Isn't it clear?

nilshomer · 06-14-2010, 12:12 PM

Quote:

Originally Posted by lh3

SAM spec: POS is "1-based leftmost POSition/coordinate of clipped sequence". Isn't it clear?

I was reading 1.4.3, since this is where you would ask such a question. Very clear, sorry

.

Bio.X2Y · 06-14-2010, 12:15 PM

Thanks guys.

lh3, I'm afraid I still find that a bit ambiguous -

does "clipped sequence" refer to the "sequence that is clipped" (implying the whole thing, including the clipped part) or the "region of the sequence that remains after clipping".

Which way are you taking it?

Thanks

Bio.X2Y · 06-14-2010, 12:38 PM

As I think about it, the second one seems to make the most sense - "region of the sequence that remains after clipping".

Thanks for your input everyone.

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06-14-2010, 11:01 AM	#1
Bio.X2Y Member Location: Europe Join Date: Apr 2010 Posts: 46	SAM Format - Hard Clip Hiya, 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. Bio.

06-14-2010, 11:34 AM	#2
mrawlins Member Location: Retirement - Not working with bioinformatics anymore. Join Date: Apr 2010 Posts: 63	I don't recall having seen a SAM file with an H at the beginning of the CIGAR, only at the end. If the H is at the end (or somehow in the middle) then it shouldn't affect the position. I would guess the position reflects the first base corresponding to the first H, though that may not be true. My reasoning is, if you're not starting from the first H, why even include the hard clipping in the first place? Since hard clipped sequence isn't included in the reported alignment, the only real reason for including it is to indicate the offset from the state position. That being said, I'm just guessing here. If somebody knows conclusively, go with whatever they tell you. Good Luck

06-14-2010, 11:45 AM	#3
Bio.X2Y Member Location: Europe Join Date: Apr 2010 Posts: 46	Thanks mrawlins! I'm leaning towards that interpretation too. I'm trying to get a definitive stance since I'm in the process of writing some code that supports sam, and I'd prefer not to add another non-compliant application to the mix! Anybody have something conclusive? Thanks for your time

06-14-2010, 12:04 PM	#5
lh3 Senior Member Location: Boston Join Date: Feb 2008 Posts: 693	SAM spec: POS is "1-based leftmost POSition/coordinate of clipped sequence". Isn't it clear?

06-14-2010, 12:15 PM	#7
Bio.X2Y Member Location: Europe Join Date: Apr 2010 Posts: 46	Thanks guys. lh3, I'm afraid I still find that a bit ambiguous - does "clipped sequence" refer to the "sequence that is clipped" (implying the whole thing, including the clipped part) or the "region of the sequence that remains after clipping". Which way are you taking it? Thanks

06-14-2010, 12:38 PM	#8
Bio.X2Y Member Location: Europe Join Date: Apr 2010 Posts: 46	As I think about it, the second one seems to make the most sense - "region of the sequence that remains after clipping". Thanks for your input everyone.