ngsF

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When should I set --Freq_fixed=TRUE in calculating inbreeding Coefficient?

3

Hi, Filipe, I am using ngsF to estimate the inbreeding coefficient for a population of giraffes. I am not sure about the parameter "--freq_fixed". The readMe stated "assume initial MAF...

wul88

Difference estimation ANGSD / ngsF

1

Hi! I tried to estimate the inbreeding coefficient for different populations using both ANGSD -doHWE option and ngsF. I use the exact same command to generate the hwe.gz and the...

jbruxaux

Number of sites in .mafs.gz different from angsd

1

Hi, is the number of sites in .mafs.gz file supposed to be different from those in angsd log file? For one of my populations I get a different value when...

bvaditi

Currently ngsF only works when all sites are variables (call SNPs first). One way would be to use a weighted average but it only seems to work with extreme weights...

fgvieira

Currently, individual loglkl is disabled since, for sake of speed, it only calculates the fast_lkl. Should implement the correct individual loglkl

fgvieira

Arbitrary ploidy to account for X/Y and poliploid. See: http://www.genetics.org/content/186/4/1367.full

fgvieira

Allow for negative F (-1 < F < 1) to accommodate other deviations from HWE

fgvieira

Implement accelerated EM method see: http://www.jstor.org/stable/2290716

fgvieira

LKL currently not threaded.

fgvieira