[KaiYe]

I have 40 bam files in config file, each 30GB, I am running each chr at one PBS job. So how much memory each job needs? Does each job read the entire BAM file into memory at once?

Pindel could take 24 ppn at one node, right?

Thanks,

as we communicated by email, you can distribute your calculation with -c chr:start-end. You might use 4 threads per job and maximize the number of jobs running at the same time. Pindel will only get the data within the specified regions than scanning everything all at once. With -w, you are able to control memory usage. What is your coverage and you are processing exome data?