Hello I'm looking for a dataset of snps from patients with breast cancer to compare with snps from normal patients. I only could find affymetrix data and it's about 7GB per patient on GWAS Studies. I would like to compare using only about 500 snps not 500k from > 100 patients.
Is there a way to download TCGA data for only a list of genes or snps ?
If you were looking for expression, copy number, mutations, etc for a list of genes, you could snag it from the Data Browser. Unfortunately, to get the raw SNP calls, you'll have to download the whole array from the data portal and subset out what you need.
FWIW, it should be much smaller than 7GB per patient, though - closer to 50 MB per patient would be more in line with what I expect. Be sure you're going either through the Bulk Download form or directly to the Https Directories so that you can grab only what you need.
(I'm also assuming that you've been cleared for TCGA access. Since SNP arrays contain information that could be used to identify a patient, they require that you request access and provide a short description of how you're using the data - more info here)
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