Hi,
Im trying to find the MSI-status for TCGA samples and couldn't find the information in clinical/clinical supplement and biospecimen/biospecimen supplement files.
What i need looks something like this:
https://wiki.nci.nih.gov/display/TCGA/Microsatellite+data
Where can I find these information in the new TCGA portal ?
MSIseq: Software for Assessing Microsatellite Instability from Catalogs of Somatic Mutations
How to obtain Microsatellite Instability (MSI) status for TCGA tumor samples:
Extracting progression models for TCGA MSI/MSS colorectal tumors from the COADREAD project with the TRONCO package
http://biorxiv.org/content/biorxiv/suppl/2015/09/23/027359.DC1/027359-2.pdf
Sheldon is right. If you use the R code that we provide with the release of the Pipeline for Cancer Inference, it will fetch all the clinical information that you need. The code has a lot of comments, and you should be able to find where we extract the MSI/MSS clinical status from TCGA data
https://sites.google.com/site/troncopackage/examples/colorectal
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version 2.3.6
Can I get TCGA somatic mutation vcf files or maf files for MSI - H, MSI-L - MSS samples?
I mean open access without any special access and authorizations?
You can get some data from GDC portal: https://portal.gdc.cancer.gov/analysis_page?app= and https://portal.gdc.cancer.gov/analysis_page?app=Downloads
Most of sensitive data types (VCF) are going to require permission.