Hi,
I want to determine the number of haplotype clusters there are in my dataset using fastphase. The results are meant to produce a _kselect file, but this never happens and fastphase always uses a K15 for the model.
This is what I have been running- I wanted to test the number of clusters from 5 to 25 going up intervals of 4
./fastPHASE -T10 -ochr26 -KL5 -KU25 -KI5 -KS5 -KM500 -KP.1 plink.chr-26.recode.phase.inp
Am I missing something?
TIA
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dp0b •
4 answers
Regarding K selection procedure described in the manual (fastPHASE 1.4), I have contacted Paul Scheet, a developer of fastPHASE. He replied that current version of the tool (fastPHASE 1.4.8) doesn't have this option more.
I write wrapper script for fastPHASE to estimate the best K. Feel free to contact me, if you are interested in testing the script for your data.
Here a workflow I created to estimate K in fastPHASE. Everybody is welcome to explore it.
Hi! I have the same problem. Did you get the solution?
My comand was this and I don´t get any _kselect file.
./fastPHASE -T20 -C30 -KL6 -KU30 -Ki2 -Ks10 -Km500 -Kp.05 -omerge_Churras280_Merino236 Chu278Mer236qc2simple.inp
Do you need to do it for a single chromosome?
Could you give me a hint? Regards, Beatriz
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