Questions tagged [snp-chip]

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2 votes
2 answers

Chosing an imputation panel for SNP-Chip data?

I have about 1,000 SNP-Chip data (samples) that I'd like to impute over (for the purpose of having more rsIDs to match against GWAS data). However, I don't know the ancestry of each sample / the ...
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3 votes
0 answers

Given a 'random' rsID, how can I find the closest (LD) SNP in a given set of SNPs?

I'm assuming that this is such a common question that I don't have to do my own imputation... I have a SNP from a paper that is associated with a specific trait... Actually I have 8 of them: https://...
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0 votes
1 answer

Where can I find a basic example for testing association between a phenotype and each of the variants of a chromosome?

I am a statistics student trying to find data suitable for a particular method. From what I have read so far, it is of interest to determine if variants within a chromosome are associated with a ...
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1 vote
1 answer

Convert SNP data from GEO into PED and MAP files?

I can easily grab SNP-Chip data from NCBI's GEO database for a given Illumina SNP-Chip array, e.g. from here: GEO provides data as SOFT ...
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4 votes
1 answer

Statistical approach to compare the SNP genotyping data among set of individuals

So, I have the genotyping data of about 650,000 SNPs for 96 individuals. I already know the Y DNA haplogroup of these individuals, so to some extent, I have a gross understanding of their ancestry. ...
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4 votes
1 answer

Compute copy number from cases and controls

I have some data on Copy Number Variation (SNP chip) for a population of samples. In particular, I have a set of samples (considered as cases) which display a specific disease phenotype, and another ...
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