Long time I am struggling how to provide GISTIC2 required input like
I have called somatic copy number by scatngs and I have copy number output file (attached);
This is few lines of scatngs copy number output
1,1,13116,665401,2,1,3,1 2,1,668374,96324627,2,1,2,1 3,1,96326095,96419709,2,1,1,0
In scatngs reference paper says in this file we have
Segment number Chromosome Start position (origin-1) End position (origin-1) Major copy number—normal Minor copy number—normal Major copy number—tumor Minor copy number—tumor
scatngs also returns another output like below
Chromosome Position Log R segmented LogR BAF segmented BAF Copy number Minor allele Raw copy number rs62635286 1 13116 -0.0290741822638953 0.245246748556562 0.25 NA 3 1 2.35806652809599 rs75454623 1 14930 0.402869048014209 0.245246748556562 0.3095 NA 3 1 4.14031506947036
I am wondering how I can get
Segment_Mean From this files?
Segment_Mean = log2(tumour copy number / 2)
So, does that mean I should add up
Major copy number—tumor and
Minor copy number—tumor to get tumour copy number? for getting Num_Probes what should I do?
scatngs uses read counts at SNPs to generate calls and so the locations of the SNPs is what I need to generate the number of markers in each segment. (eg each SNP = 1 marker).
Do they mean, for instance if the position of SNP rs62635286 is 13116, so the num_prob is 13116?
Any help please?
Thanks a lot in advance