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-   -   Expected insertion: deletion ratio for exome data? (http://seqanswers.com/forums/showthread.php?t=28330)

chongm 03-12-2013 06:43 PM

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

adaptivegenome 03-12-2013 07:42 PM

It common to see a deletion bias with the reference. Insertions are harder to map.

chongm 03-12-2013 07:47 PM

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?

adaptivegenome 03-12-2013 07:51 PM

Quote:

Originally Posted by chongm (Post 98955)
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.

chongm 03-12-2013 07:57 PM

Quote:

Originally Posted by adaptivegenome (Post 98957)
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.

adaptivegenome 03-12-2013 08:03 PM

Quote:

Originally Posted by chongm (Post 98959)
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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