Hello, 

I downloaded mutation data from TCGA from here: http://firebrowse.org/  select SKCM >SNP6_copynum

and the data looks as follows:

        Sample	Chromosome	Start	End	Num_Probes	Segment_Mean
    TCGA-3N-A9WB-10A-01D-A38I-01	1	61735	534551	31	-0.3442
    TCGA-3N-A9WB-10A-01D-A38I-01	1	564621	16345255	8476	0.0159
    TCGA-3N-A9WB-10A-01D-A38I-01	1	16363940	16389566	8	0.8209


Is there a way I can find out which type of mutations these are? I tried looking at the SNP6 manifest and could not get that information either.


Thank you!!
It is processed (by GISTIC 2.0, I believe) copy number data derived from Affymetrix SNP 6.0 microarray, which has probes that target both SNPs and copy number variants. It is a commonly used platform for determining genome-wide CNV profiles (I used it during  my PhD in breast cancer).

Note that you may want to instead download the file with '*minus_germline_cnv*' in its name, i.e., download it from Firebrowse.

If you want to process it, take a look here:

 1. <a href="https://www.biostars.org/p/311199/#311746">Part I</a>
 2. <a href="https://www.biostars.org/p/341792/#341805">Part II</a>
 3. <a href="https://www.biostars.org/p/311199/#311444">Part III</a>

Kevin