Hi Everyone
I'm using fastPHASE v.1.4.8 to estimate haplotypes on a UNIX cluster. I have provided the -F
flag to get haplotype frequencies and the _freqs
file is being returned without those frequencies. Does the -F
flag need to interact with any other input files or flags for it to produce freqs? I've tried a few different iterations of supplying positive values behind -F
, no -F
, -F
with the default #iterations, etc. No luck.
Does the pop_labels file need to contain both poplabels on a row and sample names? Seems like that's not the case given the description of the pop_labels file in the manual v1.4.
This is my command:
./fastPHASE -T20 -C45 -F5000 -upop_labels -q0.9 -w -Pm -Pp -KU30 -KL5 -Ki5 -o./ input.inp
Which produces this _freqs file:
> estimated sample haplotype frequencies for entire sample
sampled.haplotype
> estimated sample haplotype frequencies for "subpopulation" 1
sampled.haplotype
> estimated sample haplotype frequencies for "subpopulation" 2
sampled.haplotype
pop_labels
is 1x89, with 46 1's and 43 2's all in a single row with a space between the lables, like so
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
Can anyone tell me a bit more about the -F and how to get the _freqs file filled with frequencies?
Thanks so much!
It seems beagle is more popular in speed and accuracy, right?
Popularity aside, I can't get -F to work
Just check whether you are latest fastPHASE. I just run it now and -F works.
hi!do you know how to use the fasephase,I can't get the freqs in output,can you give me some advises.