Post date: May 29, 2015 6:8:28 PM
I want to see how my results using popanc compare to the linkage model with admixture in structure. This seems like a nice option as it uses an classic HMM approach but doesn't require known phase or reference haplotypes. I have the demographic data sets running now with structure 2.3.4. The parameter files and results will be in /labs/evolution/projects/popanc_sims/structure/. The MCMC is 10,000 burnin plus 10,000 steps for sampling parameters, with 2 chains per data set. The content from mainparams and extraparams is below:
KEY PARAMETERS FOR THE PROGRAM structure. YOU WILL NEED TO SET THESE
IN ORDER TO RUN THE PROGRAM. VARIOUS OPTIONS CAN BE ADJUSTED IN THE
FILE extraparams.
"(int)" means that this takes an integer value.
"(B)" means that this variable is Boolean
(ie insert 1 for True, and 0 for False)
"(str)" means that this is a string (but not enclosed in quotes!)
Basic Program Parameters
#define MAXPOPS 2 // (int) number of populations assumed
#define BURNIN 10000 // (int) length of burnin period
#define NUMREPS 10000 // (int) number of MCMC reps after burnin
Input/Output files
#define INFILE infile // (str) name of input data file
#define OUTFILE outfile //(str) name of output data file
Data file format
#define NUMINDS 150 // (int) number of diploid individuals in data file
#define NUMLOCI 20002 // (int) number of loci in data file
#define PLOIDY 2 // (int) ploidy of data
#define MISSING -9 // (int) value given to missing genotype data
#define ONEROWPERIND 1 // (B) store data for individuals in a single line
#define LABEL 0 // (B) Input file contains individual labels
#define POPDATA 1 // (B) Input file contains a population identifier
#define POPFLAG 1 // (B) Input file contains a flag which says
whether to use popinfo when USEPOPINFO==1
#define LOCDATA 0 // (B) Input file contains a location identifier
#define PHENOTYPE 0 // (B) Input file contains phenotype information
#define EXTRACOLS 0 // (int) Number of additional columns of data
before the genotype data start.
#define MARKERNAMES 0 // (B) data file contains row of marker names
#define RECESSIVEALLELES 0 // (B) data file contains dominant markers (eg AFLPs)
// and a row to indicate which alleles are recessive
#define MAPDISTANCES 1 // (B) data file contains row of map distances
// between loci
Advanced data file options
#define PHASED 0 // (B) Data are in correct phase (relevant for linkage model only)
#define PHASEINFO 0 // (B) the data for each individual contains a line
indicating phase (linkage model)
#define MARKOVPHASE 0 // (B) the phase info follows a Markov model.
#define NOTAMBIGUOUS -999 // (int) for use in some analyses of polyploid data
EXTRA PARAMS FOR THE PROGRAM structure. THESE PARAMETERS CONTROL HOW THE
PROGRAM RUNS. ATTRIBUTES OF THE DATAFILE AS WELL AS K AND RUNLENGTH ARE
SPECIFIED IN mainparams.
"(int)" means that this takes an integer value.
"(d)" means that this is a double (ie, a Real number such as 3.14).
"(B)" means that this variable is Boolean
(ie insert 1 for True, and 0 for False).
PROGRAM OPTIONS
#define NOADMIX 0 // (B) Use no admixture model (0=admixture model, 1=no-admix)
#define LINKAGE 1 // (B) Use the linkage model model
#define USEPOPINFO 1 // (B) Use prior population information to pre-assign individuals
to clusters
#define LOCPRIOR 0 //(B) Use location information to improve weak data
#define FREQSCORR 0 // (B) allele frequencies are correlated among pops
#define ONEFST 0 // (B) assume same value of Fst for all subpopulations.
#define INFERALPHA 1 // (B) Infer ALPHA (the admixture parameter)
#define POPALPHAS 0 // (B) Individual alpha for each population
#define ALPHA 1.0 // (d) Dirichlet parameter for degree of admixture
(this is the initial value if INFERALPHA==1).
#define INFERLAMBDA 0 // (B) Infer LAMBDA (the allele frequencies parameter)
#define POPSPECIFICLAMBDA 0 //(B) infer a separate lambda for each pop
(only if INFERLAMBDA=1).
#define LAMBDA 1.0 // (d) Dirichlet parameter for allele frequencies
PRIORS
#define FPRIORMEAN 0.01 // (d) Prior mean and SD of Fst for pops.
#define FPRIORSD 0.05 // (d) The prior is a Gamma distribution with these parameters
#define UNIFPRIORALPHA 1 // (B) use a uniform prior for alpha;
otherwise gamma prior
#define ALPHAMAX 10.0 // (d) max value of alpha if uniform prior
#define ALPHAPRIORA 1.0 // (only if UNIFPRIORALPHA==0): alpha has a gamma
prior with mean A*B, and
#define ALPHAPRIORB 2.0 // variance A*B^2.
#define LOG10RMIN -4.0 //(d) Log10 of minimum allowed value of r under linkage model
#define LOG10RMAX 1.0 //(d) Log10 of maximum allowed value of r
#define LOG10RPROPSD 0.1 //(d) standard deviation of log r in update
#define LOG10RSTART -2.0 //(d) initial value of log10 r
USING PRIOR POPULATION INFO (USEPOPINFO)
#define GENSBACK 2 //(int) For use when inferring whether an indiv-
idual is an immigrant, or has an immigrant an-
cestor in the past GENSBACK generations. eg, if
GENSBACK==2, it tests for immigrant ancestry
back to grandparents.
#define MIGRPRIOR 0.001 //(d) prior prob that an individual is a migrant
(used only when USEPOPINFO==1). This should
be small, eg 0.01 or 0.1.
#define PFROMPOPFLAGONLY 1 // (B) only use individuals with POPFLAG=1 to update P.
This is to enable use of a reference set of
individuals for clustering additional "test"
individuals.
LOCPRIOR MODEL FOR USING LOCATION INFORMATION
#define LOCISPOP 1 //(B) use POPDATA for location information
#define LOCPRIORINIT 1.0 //(d) initial value for r, the location prior
#define MAXLOCPRIOR 20.0 //(d) max allowed value for r
OUTPUT OPTIONS
#define PRINTNET 1 // (B) Print the "net nucleotide distance" to screen during the run
#define PRINTLAMBDA 1 // (B) Print current value(s) of lambda to screen
#define PRINTQSUM 1 // (B) Print summary of current population membership to screen
#define SITEBYSITE 1 // (B) whether or not to print site by site results.
(Linkage model only) This is a large file!
#define PRINTQHAT 0 // (B) Q-hat printed to a separate file. Turn this
on before using STRAT.
#define UPDATEFREQ 100 // (int) frequency of printing update on the screen.
Set automatically if this is 0.
#define PRINTLIKES 0 // (B) print current likelihood to screen every rep
#define INTERMEDSAVE 0 // (int) number of saves to file during run
#define ECHODATA 1 // (B) Print some of data file to screen to check
that the data entry is correct.
(NEXT 3 ARE FOR COLLECTING DISTRIBUTION OF Q:)
#define ANCESTDIST 0 // (B) collect data about the distribution of an-
cestry coefficients (Q) for each individual
#define NUMBOXES 1000 // (int) the distribution of Q values is stored as
a histogram with this number of boxes.
#define ANCESTPINT 0.90 // (d) the size of the displayed probability
interval on Q (values between 0.0--1.0)
MISCELLANEOUS
#define COMPUTEPROB 1 // (B) Estimate the probability of the Data under
the model. This is used when choosing the
best number of subpopulations.
#define ADMBURNIN 500 // (int) [only relevant for linkage model]:
Initial period of burnin with admixture model (see Readme)
#define ALPHAPROPSD 0.025 // (d) SD of proposal for updating alpha
#define STARTATPOPINFO 0 // Use given populations as the initial condition
for population origins. (Need POPDATA==1). It
is assumed that the PopData in the input file
are between 1 and k where k<=MAXPOPS.
#define RANDOMIZE 1 // (B) use new random seed for each run
#define SEED 2245 // (int) seed value for random number generator
(must set RANDOMIZE=0)
#define METROFREQ 10 // (int) Frequency of using Metropolis step to update
Q under admixture model (ie use the metr. move every
i steps). If this is set to 0, it is never used.
(Proposal for each q^(i) sampled from prior. The
goal is to improve mixing for small alpha.)
#define REPORTHITRATE 0 // (B) report hit rate if using METROFREQ