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Unique SNP sharing between populations

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
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updated by Ram Ram • written by always_learning always_learning

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?

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updated by Ram Ram • written by hgibriel • hgibriel

1 answer

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

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updated by Ram Ram • written by fadsfadfdsafdasfdsa fadsfadfdsafdasfdsa

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