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Posts by nick.carleson
Answer: A: GATK: -nct and -nt
... Hmm that is not my understanding, but I could be reading the help docs wrong. I think -nct will still use the same number of CPU cores as if you were specifying -nt. So in your example, both would use 8 cores; it's just that those 8 cores would be controlled by a single "mother" thread. System memor ...
... It's also possible your original BAM kept the unmapped reads, and when you split the BAM into chromosomes the unmapped reads had nowhere to go. ...
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