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Dear All,
I am trying to optimise Pindel to run on a small set of 12 whole exome samples to detect structural variants. With the latest build of Pindel-0.2.5, I am running the following commands -
pindel -f /path/to/refhg19 -i /path/to/config -j /path/to/probes_bed_file -T 2 -x 2
To shorten the runtime, I have split the probes file such that each chromosome has a separate bed files. Thus with the given command, pindel spawns 24 threads on 12 cores.
My problem is despite this setup, it takes about ~48 hrs to complete the analysis. Can someone please suggest me a more efficient strategy to shorten the run time? Or is this is an expected and acceptable runtime?
Any responses are appreciated.
Thanks.
Best,
sBugs
I am trying to optimise Pindel to run on a small set of 12 whole exome samples to detect structural variants. With the latest build of Pindel-0.2.5, I am running the following commands -
pindel -f /path/to/refhg19 -i /path/to/config -j /path/to/probes_bed_file -T 2 -x 2
To shorten the runtime, I have split the probes file such that each chromosome has a separate bed files. Thus with the given command, pindel spawns 24 threads on 12 cores.
My problem is despite this setup, it takes about ~48 hrs to complete the analysis. Can someone please suggest me a more efficient strategy to shorten the run time? Or is this is an expected and acceptable runtime?
Any responses are appreciated.
Thanks.
Best,
sBugs
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