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Old 12-18-2009, 08:07 AM   #1
kakar_nipun
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Location: texas,us

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Default Calling indels from samtools-pileup

Hi Guys

I was not clear on the samtools indel calling documentation, and therefore wanted to clarify a few things. I observe the following cases in my samtools-indel calling output.

chr10 215923 * +G/* 943 1614 59 84 +G * 1 83 0 0 0

chr10 278061 * */+G 284 284 60 24 * +G 23 1 0 0 0

chr10 257113 * +GCAAG/+GAC 266 1710 59 88 +GCAAG +GAC 1 1 86 11 26

I am unable to understand the difference between the first and the second case; according to me both show an insertion of one base(G). However what i am not clear about is the difference between :+G/* and */+G.?

Regarding the third case shown above, the question is kind of related to the above question. What does +GCAAG/+GAC mean?. Looking at the no. reads columns it seems,
1 read saw +GCAAG
1 read saw +GAC
but, what is the third allele in this case, as there are 86 reads seeing some third allele.?
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Old 01-22-2010, 05:41 AM   #2
dnusol
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Location: Spain

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Default

Chech the SAM FAQ for samtools on page 2. There is no difference in the two results.

To me, +GCAAG/+GAC seems to be that there could be a het insertion, but I cannot guess what the third allele value could indicate.

HTH
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Old 01-21-2011, 03:31 AM   #3
Gangcai
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Location: Shanghai, China

Join Date: Nov 2009
Posts: 30
Default Unclear about Indels calling in samtools pileup file

Hi everyone,
Has anybody solved the problem already? I also meet the same problem. In my case,
I want to know if an Indel is homozygous or heterzygous. The pileup file(from Sanger SNP pileup file) looks like this:
1 3000648 * -CTTACA/* 367 747 58 17 -CTTACA * 11 6 00 0

1 3004544 * -C/-C 71 381 60 11 -C * 8 3 0 00

My question is how does it look like for all the 17 and 11 reads mapped? Are all of them have such deletions?

Quote:
Originally Posted by kakar_nipun View Post
Hi Guys

I was not clear on the samtools indel calling documentation, and therefore wanted to clarify a few things. I observe the following cases in my samtools-indel calling output.

chr10 215923 * +G/* 943 1614 59 84 +G * 1 83 0 0 0

chr10 278061 * */+G 284 284 60 24 * +G 23 1 0 0 0

chr10 257113 * +GCAAG/+GAC 266 1710 59 88 +GCAAG +GAC 1 1 86 11 26

I am unable to understand the difference between the first and the second case; according to me both show an insertion of one base(G). However what i am not clear about is the difference between :+G/* and */+G.?

Regarding the third case shown above, the question is kind of related to the above question. What does +GCAAG/+GAC mean?. Looking at the no. reads columns it seems,
1 read saw +GCAAG
1 read saw +GAC
but, what is the third allele in this case, as there are 86 reads seeing some third allele.?

Last edited by Gangcai; 01-21-2011 at 03:34 AM.
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