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Old 03-12-2013, 06:43 PM   #1
chongm
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Default Expected insertion: deletion ratio for exome data?

Hi Everyone,

I am wondering what the expected insertion: deletion ratio is for your exomes? Right now I'm getting ~0.9 meaning deletions are a bit more common than insertions in the exome? Is there a reason for this?

Thanks,

MC
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Old 03-12-2013, 07:42 PM   #2
adaptivegenome
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It common to see a deletion bias with the reference. Insertions are harder to map.
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Old 03-12-2013, 07:47 PM   #3
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Thanks for the reply. So biologically there is no reason for there to be more deletions than insertions and so this ratio should approach 1. This is probably a naiive question but why are insertions more difficult to map then deletions?
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Old 03-12-2013, 07:51 PM   #4
adaptivegenome
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Quote:
Originally Posted by chongm View Post
Thanks for the reply. So biologically there is no reason for there to be more deletions than insertions and so this ratio should approach 1. This is probably a naiive question but why are insertions more difficult to map then deletions?
No its a good question. If you have a read of fixed length and it spans an insertion then you have less sequence that can be used to map the read to the reference.
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Old 03-12-2013, 07:57 PM   #5
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Quote:
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No its a good question. If you have a read of fixed length and it spans an insertion then you have less sequence that can be used to map the read to the reference.
I see, whereas in the case of a deletion all bases will map to the read reference.
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Old 03-12-2013, 08:03 PM   #6
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Quote:
Originally Posted by chongm View Post
I see, whereas in the case of a deletion all bases will map to the read reference.
Yes, and of course there are other factors that affect indel recall as well (like gap penalty and extension penalty, etc.)...
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