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Memory heap size problem with Haplotype caller
I am trying to run HaplotypeCaller on my processed bam file but it keeps running out of memory.
I have tried increasing the heap size to 90G but it still crash. This might have to do with the type of analysis I am doing...
The sample are pool of pigs (6 individual so a ploidy of 12 for this particular sample) that have been sequenced on targeted regions, I use the bed file that has been given with the kit to narrow done the calling to the targeted regions. I have also reduce the number of alternative allele from 6 to 3. But it still crash after a while. Is there any other parameters I should try to modify to reduce the memory usage?
I have attached the log file if you want to have a look at all the parameters.