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Old 12-14-2015, 12:28 PM   #4
Richard Finney
Senior Member
 
Location: bethesda

Join Date: Feb 2009
Posts: 700
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Copy number can be guestimated from SNP6 data.

See this post ...
https://www.biostars.org/p/112310/

Example file from
http://tcga-data.nci.nih.gov///tcgaf...v_hg19.seg.txt

It looks like this ...
Sample Chromosome Start End Num_Probes Segment_Mean
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 1 3218610 59982831 30896 0.005
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 1 59983689 59983731 2-1.8298
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 1 59987818 247813706 97244 4e-04
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 2 484222 85332445 48655 0.0055
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 2 85332460 85333406 2-1.9034
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 2 85333976 242476062 81598 0.0048
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 3 2212571 197538677 105526 3e-04
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 4 1053934 188762240 101844 6e-04
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 5 914233 41791600 24110 0.0018
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