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I'm currently using DepthOfCoverage with -L option and a BED intervals file. I would to get gene report also. I'm not familiar with RefSeq format for the gene list.
I work with HGNC and Ensembl genes. I could get a gene list file with the following format:
HGNC chr start end
But this doesn't seem to work. Any suggestions on how I could achieve that or how I could generate a valid gene list file with my current intervals?