I am running the somatic variant caller in VarScan on several files. On average, the input .pileup files are ~50 GB each (with both tumor and normal samples).
I've noticed that I've gotten the following error when running some samples:
Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit
It doesn't happen for all files, and there still SNP and indel calls produced for samples that show this error. So, I would have to parse the error log if I wanted to go back and figure out which samples might be missing some variants.
Does anybody have a recommendation about how much memory should be allocated to java when running VarScan (with two ~50 GB .pileup file as the input)? I'm hoping that this can help avoid getting the error message.