Question: How can I get alleles about each sample?
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gravatar for haruomomo.goo
22 months ago by
haruomomo.goo0 wrote:

I want to get genotypes of the SNP in each sample from 1000 genomes phase3 .tped or .ped files. How should I do by plink?

like:

about rs1000000
sampleID familyID allele1 allele2

I look forward to hearing from you.

snp plink gene • 495 views
ADD COMMENTlink modified 22 months ago by Kevin Blighe60k • written 22 months ago by haruomomo.goo0
0
gravatar for Kevin Blighe
22 months ago by
Kevin Blighe60k
Kevin Blighe60k wrote:

Please follow this and you will then have obtained all of the final release of the 1000 Genomes Phase III data in both VCF and PLINK format: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format

You can use the PED file that's also downloaded for the purposes of seeing in which populations your variant of interest is present.

Other [easier] ways of looking up variant allele frequency information exist outside of PLINK:

Then there are also annotation tools, like ANNOVAR and VEP, which can automatically annotate lists of variants with information from 1000 Genomes.

Kevin

ADD COMMENTlink written 22 months ago by Kevin Blighe60k
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