TCGA: SNPs level 2

Question

[ilana.sychikov]

Hi everyone,

I would like to get snp level 2 data (https://wiki.nci.nih.gov/display/TCGA/SNP+array-based+data) from TCGA (breast cancer). Unfortunately, TCGA site is down for maintenance, and the data available in the genomic data commons (https://gdc-portal.nci.nih.gov/), but I can't find it there. Can someone help me to find it? Is it possible that not all data is available there?

Thank you, Ilana

[seth]

I had this issue as well with level 2 SNP data, I emailed https://gdc.nci.nih.gov/support and after some work on their part they provided me with a manifest file to be used with the gdc-client.

[ilana.sychikov]

Thank you, it helped!