Question: Unique SNP sharing between populations
2
gravatar for always_learning
6.0 years ago by
always_learning1.0k
Doha, Qatar
always_learning1.0k wrote:

Dear All, 

 

I am looking out to find out Unique SNP sharing between populations means common SNPs between a set of populations. I have merged set of VCF containing all population. What will be the possible workaround for this ? Each populations have several individuals. for exam we have Chinese population which consists of 5 samples VCF and then merge it into single VCF files which I call as population VCF. similarly we have for other's population too. I am thinking of using VCF tools (VCF-isec) to find the matching shared SNP between populations.

Can you guys suggest any other possible way apart from this also ? I mean can we get something from "FORMAT" section of VCF based on presence of population info ? 

snp • 3.1k views
ADD COMMENTlink modified 2.3 years ago by hgibriel10 • written 6.0 years ago by always_learning1.0k
1
gravatar for hgibriel
2.3 years ago by
hgibriel10
hgibriel10 wrote:

I do have the same question! So I first used GATK to call SNPs for a each isolate in a population. Next, I joined all SNPs in a population with GenotypeGVCfs. Now I need to select only SNPs that are shared by all isolates. Can u guys suggest how I can do so?

ADD COMMENTlink written 2.3 years ago by hgibriel10
0
gravatar for always_learning
6.0 years ago by
always_learning1.0k
Doha, Qatar
always_learning1.0k wrote:

Any experts ? Please !!

ADD COMMENTlink written 6.0 years ago by always_learning1.0k
0
gravatar for vlaufer
6.0 years ago by
vlaufer280
United States
vlaufer280 wrote:

Try this.

Find the tool Lanc-CSV. It is a local ancestry estimation software. 

Download their reference data files for each chromosome.

Everything marked 1 2 or 3 is a continent specific marker.

Everything marked -99 shows up in more than one population.

take all of those files, do grep "-99" $FILE > mixmarkersonly.$FILE

Alternatively could write an awk script to process UCSC SNP output from their table browser

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by vlaufer280
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