How to run an identity-by-descent calculation on plink with a p-value threshold?
I've already run an SNP filter using plink on map and pedigree files, now I want to run IBD with a p<.01 threshold. What is the syntax? The --pcc option won't take.
While we're at it, what documentation on plink do you prefer?
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from the mountains
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The name of the flag is --ppc, not --pcc. Let me know if you still have problems getting that to work.
As for documentation, I recommend using the PLINK 1.07 website as the primary reference when you're unfamiliar with a command. I wrote the PLINK 1.9 documentation under the assumption that the reader was already familiar with 1.07. (This situation will improve when PLINK 2.0 is mostly complete; until then, coding takes priority over writing.)
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