Question

Reference Data Set Download from 1000 genomes

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4.5 years ago

karthick.n ▴ 10

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

1000genomes • 1.4k views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 4.5 years ago by karthick.n ▴ 10

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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 REPLY • link updated 4.5 years ago by GenoMax 147k • written 4.5 years ago by karthick.n ▴ 10

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

ADD REPLY • link 4.5 years ago by Yean ▴ 140

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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 REPLY • link 4.5 years ago by GenoMax 147k

score 0 · Answer 1 · 2020-05-12

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4.5 years ago

Yean ▴ 140

Please check Kevin's tutorial

ADD COMMENT • link 4.5 years ago by Yean ▴ 140

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Thank you very much! Yean.

Best, Karthick

ADD REPLY • link 4.5 years ago by karthick.n ▴ 10