Probes meta file from broadinstitute website for Copy Number Variation Analysis (CNV) analysis for a list of samples

[MaryGoAround]

Hello

I have a list of samples from TCGA which clinical data says they have not received chemotherapy

I have tried to use segmentation and marker file from firehose to be able to run gistic only on my list of samples but likely marker file is not compatible with marker file and says

[fi1drt@cyan01 man]$ ./run_gistic_test
--- creating output directory ---
--- running GISTIC ---
Setting Matlab MCR root to /temp/hgig/fi1d18/man/MATLAB_Compiler_Runtime
GISTIC version 2.0.23
 
GISTIC 2.0 input error detected:
80177 segment start or end positions in '/temp/hgig/fi1d18/man/seg/seg.txt' do not match any markers in '/temp/hgig/fi1drt/man/seg/marker.txt'.
First bad position is 6:170903919 at line 21.

It there any way to get prob file for a list of samples?