I'm trying to run Pindel on some whole exome tumor/normal pairs. BAMs are about ~40Gb in size. I've got a bad_alloc error at my first trial. Below is the command line. I set the window size to 1; also disabled search for breakpoints and long insertions as suggested in the FAQ:
pindel -f ucsc.hg19.fasta -i config.txt -o test -w 1 -l false -k false
Here's the output:
Initializing parameters... Pindel version 0.2.5a3, Oct 24 2013. Loading reference genome ... terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped)
I'm using 32bit Ubuntu 12.04 with 8Gb RAM, ~6Gb free.