Question: Getting ancestral states for SNP chip data for running selscan software
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gravatar for JMR
4.3 years ago by
JMR140
London - United Kingdom
JMR140 wrote:

I want to use a software for detecting signals of positive selection using genome-wide SNP data. As input data I need the ancestral and derived state for each SNP present in my data.

I found this FAQ http://www.ncbi.nlm.nih.gov/books/NBK44409/#Build.how_do_i_determine_if_a_snp_is_an which points to a file which has the ancestral state for over 60 million SNPs.

I found almost all my SNPs present on that file, but when I was checking the ancestral alleles I encountered two problems:

First, some ancestral alleles didn't match my file. For example in my data SNP 21 rs17003832 22619035 C A, is either C or A. But the ancestral data file points to rs17003832 which has a T

Second some alleles in the ancestral data file had two SNPs reported as ancestral, for example:

rs16997069 C
rs16997069 T

So what should I do? Maybe the first problem could be solved by a strand flip but what about the second one?

Any help would be greatly appreciated.

 

snp selection • 1.3k views
ADD COMMENTlink written 4.3 years ago by JMR140

For your first question, maybe check out the version of the reference data.

BTY, I have the same question as yours,and wonder what you had done with the SNPs not in the ancestral alleles data?

 

ADD REPLYlink written 4.3 years ago by Jie Ping20

Thanks for the comment. Yes, I checked the reference data and now I am working with the ancestral data for my assembly. Alas, I still got some rsSNPs with two ancestral alleles in that file. I am not sure what that problem could be. Maybe some discrepancies in different outgroups used as ancestral? I am planning to drop all SNPs with this problem, as well as those not present in this file. For the problem where I didn't got an exact match I am planning to first flip the strand and see if it then matches or else drop them. You could also check manually in the dbSNP website to see if its really a strand flip problema.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by JMR140
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