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Old 11-25-2015, 06:21 AM   #1
Location: North Carolina

Join Date: Jan 2010
Posts: 82
Default psmc bootstrap

Hi All,

I'm messing around with PSMC a bit.

I'm having trouble getting the bootstrap part to run properly. I'm sort of wondering if bwa/samtools updates are causing some issues.

The program seems to run fine for the full analysis (though I don't know if my results are reasonable or not), but I am getting division by zero errors when I try to do the bootstrap.

Seems like a lack of heterozygous sites can cause this, but that does not seem to be my issue as I have "K" sites in my psmcfa file. The problem comes in the psmc.plot step, not in the psmc run.

I know Heng Li is encouraging people to move on from PSMC, and perhaps that is reasonable, but still would like to sort this out.


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