Questions tagged [snp-chip]
The snp-chip tag has no usage guidance.
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Does pooled sample genotyping microarray analysis exist?
I want to genotype samples in small batches with a common microarray (e.g., the GSA). However, the cost is very high for small batches.
With a higher sample throughput/volume, per sample cost becomes ...
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How to get cytoband and gene level copy number from genome wide SNP array copy number data?
I have (human) Illumina genome wide SNP array copy number data. For each SNP genomewide, I have Log R Ratio (LRR) and B Allele Frequency (BAF).
What tool(s) can I use to get the integer copy numbers (...
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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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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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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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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:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52147
GEO provides data as SOFT ...
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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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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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