Re: [Samtools-help] SAMtools pileup file contains lots of "*"

[Dave L. <dl...@ge...>]

       From my experience, IGV reports the number of bases at a position 
whereas Samtools reports the number of reads crossing a position, 
regardless of whether or not those reads contain a base at the position. 
You can verify this by counting the number of *s in your Samtools line. 
I count 726. That would leave you with 96 reads with a physical base 
there. I think you have already determined this though.
     Both Samtools and IGV are reporting deleted bases at this position 
so it seems clear that you have a deletion. Is the deletion just not 
being reported by Samtools at all? Samtools reports deletions at the 
position immediately preceeding the first deleted base. Thus, if this 
was a one base pair deletion I'd expect you to have a deletion reported 
at 14172876, not 14172877. Based on what you've written, it's also 
possible that there's a multiple base pair deletion. In that case the 
deletion generating the * characters in your pileup would be even 
farther away. Could you elaborate a bit more about your lack of a 
Samtools indel call and the size of your indel?

Dave

On 09/28/2010 11:30 AM, Joseph Fass wrote:
>
> what about tview?..  it's a samtools tool, so comparing how it sees 
> this region (that samtools pileup seems to be doing funny things with) 
> to IGV might be interesting?
>
>> On Sep 28, 2010 8:20 AM, "Cliff Yiu" <mm...@ho... 
>> <mailto:mm...@ho...>> wrote:
>>
>> it is Illlumina GAIIx, SE76, BWA mapping, SAMtools SNP-calling. IGV 
>> showed the total count for this position is about 100 rather than 
>> 822. It looks like in IGV there are lots of deletion in those reads 
>> for this position.
>>
>>
>>
>> ________________________________
>> From: jos...@gm... <mailto:jos...@gm...>
>>
>> Date: Mon, 27 Sep 2010 13:10:35 -0700
>>
>>
>> Subject: Re: [Samtools-help] SAMtools pileup file contains lots of "*"
>> To: mm...@ho... <mailto:mm...@ho...>
>> CC: ...
>>
>
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