Providing input for GISTIC2
Hi,
I called somatic copy number by scatngs https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097604/#S15
That returns an output name copynumber.caveman.csv
This is few line of this file
1 1 13116 665401 2 1 3 1
2 1 668374 96324627 2 1 2 1
3 1 96326095 96419709 2 1 1 0
4 1 96421112 103508275 2 1 2 1
I want to run GISTIC2 that needs Seg.CN (log2() -1 of copy number), anybody knows how to obtain this values from scatngs output?
Thank you
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Please refer to post on Bioinformatics SE: https://bioinformatics.stackexchange.com/questions/7499/getting-this-information-for-gistic2