I have WES bam files from tumour samples and a normal sample of one patient, and I would like to estimate the tumour purity of the tumour samples with ABSOLUTE. They say that "you can supply a tab delimited segmentation file (e.g. from array CGH or massively parralel sequencing experiments) - this file must contain the columns "Chromosome", "Start", "End", "Num_Probes" and "Segment_Mean".".
I have already analysed copy number alterations (CNAs) using CopywriteR and it gives me a read_counts file with "Chromosomes", "Start", "End" and the read counts for the samples but I don't see where to get the "Num_probes" and the "Segment_Mean" information.
I would highly appreciate your help