Hi, I was wondering about the memory requirements? I'm running BaseRecalibrator step and hit an insufficient memory error. I need to pass the -Xmx option to java. What values are recommended for various GATK commands that are typically used in variant detection pipeline (HaplotypeCaller etc). It would be especially nice to know this as a function of number of reads. Thanks in advance
I tried to use DepthOfCoverage to figure out the coverage of 50 whole exome sequencing data. It works fine for single sample, however, the program always complained about memory issue, even I provide 100 GB as "-Xmx100g". Any suggestions for the problem? There is a option "--read_buffer_size", which seems to be helpful, how should set the value ?
Is there any rule of thumb for allocating memory through "bsub" for running DataProcessingPipeline per bam file or per number of reads ?