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Old 01-19-2012, 03:46 AM   #1
kjaja
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Default question related to Annovar annotation

Hi,

I am looking to filter out the variants that lie on a segmental duplication and the ones that are not in a conserved region. I have used Annovar to annotate the variants and it provides a score for the conservation and a value for the segmental duplication. I do not understand these values, can someone explain what they mean? What cutoff should I be using for my purposes?

thanks
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Old 01-19-2012, 04:44 AM   #2
Heisman
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I think it pulls those values from the UCSC genome browser, so try to find the page there that describes them.
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Old 02-20-2012, 09:51 PM   #3
neha
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Default Unknown Function SNP in annovar

Hello everyone,

I have exome data with me. I have found out the no of SNP in it. Now I want to do the functional annotation of these SNP. I choose to to that through annovar. I did gene based annotation. For exonic SNP software classifies whether they are synonymous, nonsynonymous, stopgain etc. but there were some with Unknown function. How to interpret those SNP.

Thanks in advance

Neha
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Old 02-21-2012, 07:03 AM   #4
Heisman
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Quote:
Originally Posted by neha View Post
Hello everyone,

I have exome data with me. I have found out the no of SNP in it. Now I want to do the functional annotation of these SNP. I choose to to that through annovar. I did gene based annotation. For exonic SNP software classifies whether they are synonymous, nonsynonymous, stopgain etc. but there were some with Unknown function. How to interpret those SNP.

Thanks in advance

Neha
Did you specify a variant allele? If not, it will give you "unknown", I think.
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Old 03-27-2012, 02:32 AM   #5
Jane M
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Hello,

I have one question, uncorrelated with the initial question. It concerns the input of Annovar.
We have to provide the chromosome, the position of the beginning of the variation, the position of the end of the variation, the reference and variant alleles.

My question is about the positions. In Annovar website, one example is provided: http://www.openbioinformatics.org/an...var_input.html. We can see that the positions of beginning and end of variants are always the same except for deletions of at least two nucleotides.

I was told recently that it is not compulsory to change beginning and end positions of the variation even in the case of deletions of at least two nucleotides. I think it is indeed the case, I've seen some examples where the annotation seems correct even if beginning and end positions are the same, but I would like some confirmations.

Thank you,
Jane
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