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Hi,

I have called somatic copy number in tumor-matched normal by scatngs

I have 3 output files, this is one output of scatngs

Chromosome Position Log R segmented LogR BAF segmented BAF Copy number Minor allele Raw copy number
rs62635286 1 13116 -1.23040761342626 0.00160351549950095 0 0.317683333333333 2 1 0.41361756890851
rs75454623 1 14930 -0.390888460751959 0.00160351549950095 0.3548 0.317683333333333 2 1 1.19149081633643

Could you please tell me which columns corresponds to

Num markers (number of markers in segment)

Seg.CN (log2() -1 of copy number)

Required as GISTIC2 input?


Also could you please give me an idea how I could install GISTIC2?

Thanks a lot in advance

Answers

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