I am looking to hopefully run GISTIC 2.0 on some CNV calls I have from sequencing data. However, the input file requires the following fields:
(1) Sample (sample name) (2) Chromosome (chromosome number) (3) Start Position (segment start position, in bases) (4) End Position (segment end position, in bases) (5) Num Markers (number of markers in segment) (6) Seg.CN (log2() -1 of copy number)
I am not sure how to fill in the "Num Markers" field, given that I only have sequencing data. I read in this link that it should be the number of heterozygous SNPs in each segment. Is there a way to get this information?