Question: Reference Data Set Download from 1000 genomes
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gravatar for karthick.n
8 months ago by
karthick.n10
karthick.n10 wrote:

Hi,

I want to perform population stratification analysis. I need to download indian genomes along with other ancestry genomes from 1000 genomes data set. How to download that. There are so many release in 1000 genomes. Can you post the link?

Regards, Karthick

download 1kg 1000genomes • 245 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by karthick.n10

Hi I have created the plink files based on the tutorial mentioned above . But the snp ids are like as follows: (chr:position:allele1:allele2). There is no rs ID. But my sample data has rsIDs. How to compare both when they have inconsistent SNP ids?

1       1:14599:T:A     0       14599   A       T
1       1:14930:A:G     0       14930   G       A
1       1:15211:T:G     0       15211   T       G
1       1:15274:A:G     0       15274   G       A
ADD REPLYlink modified 8 months ago by GenoMax95k • written 8 months ago by karthick.n10

Try SnpSift to annotate rsID based on your position in vcf file http://snpeff.sourceforge.net/SnpSift.html#annotate

ADD REPLYlink written 8 months ago by Yean130

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

ADD REPLYlink written 8 months ago by GenoMax95k
0
gravatar for Yean
8 months ago by
Yean130
Bangkok
Yean130 wrote:

Please check Kevin's tutorial

ADD COMMENTlink modified 8 months ago • written 8 months ago by Yean130

Thank you very much! Yean.

Best, Karthick

ADD REPLYlink written 8 months ago by karthick.n10
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