Hi everyone,

I want to get the exact copy number of each gene for each sample in PCAWG

I have located this PCAWG directory https://dcc.icgc.org/releases/PCAWG/consensus_cnv/gene_level_calls

However, there are three files listed there:

1. all_samples.consensus_CN.by_gene.170214.txt.gz
2. all_samples.consensus_CN.minor_allele.by_gene.170313.txt.gz
3. all_samples.consensus_level_calls.by_gene.170214.txt.gz

I cannot find any description of these files anywhere on the internet, can somebody give me enlightenment of what each of these files represent?

I want to obtain the copy number of each gene for each sample, and use that as a covariate for differential gene expression calling

For example, this is what the 3rd file contains:

Thank you so much!!