it happens with CombineGVCFs, I didn't check other functions.
Running in the current dir /site/ne/data/ngs/var, the error will be
ERROR MESSAGE: Couldn't read file /site/ne/data/ngs/var because file does not exist
It took me a while to figure out it's due to the empty line.
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?