out of memory

[gmachaj]

Hi,

I'm trying to run your script on my bam file but the process dies due to memory lack (32GB RAM). I have partial output file my_sample.var with variants for 5 out of 9 chromosomes and I'm wondering is there any way to run script starting from chr6? (and then combine 2 output files). Or maybe there is some other way (e.g. saving data in temp. file rather than store in RAM) to overcome the memory problem. I am also wondering if my partial var. file is already filtered or should I filter them before further processing?

Best regards,

[wushyer]

You can split the genome into several chromosomes and get the mapping bam files from each chromosome. Use one linux command to run them all and combine the result.