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minimal.ini
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;; comment out or change as desired
;; 1 = true, 0 = false
[General]
debug=0
[ParseGenotypeFile]
untypedAllele=****
;; valid fields in population header block
validPopFields=labcode
method
ethnic
contin
collect
latit
longit
complex
;; designates field name that holds population name
popNameDesignator=+
;; designates field name that holds allele data
alleleDesignator=*
;; valid fields for sample data block
validSampleFields=+populat
id
*a_1
*a_2
*c_1
*c_2
*b_1
*b_2
*dra_1
*dra_2
*drb1_1
*drb1_2
*dqa1_1
*dqa1_2
*dqb1_1
*dqb1_2
*dpa1_1
*dpa1_2
*dpb1_1
*dpb1_2
[HardyWeinberg]
lumpBelow=5
[HardyWeinbergGuoThompsonMonteCarlo]
monteCarloSteps=100000
[HomozygosityEWSlatkinExact]
;; use section if the Monte Carlo approximation to the Slatkin exact
;; Ewens-Watterson test should be run
numReplicates=10000
[Emhaplofreq]
;; comma (',') separated haplotypes blocks for which to estimate
;; haplotypes, within each "block", each locus is separated by colons
;; (':') e.g. dqa1:dpb1,drb1:dqb1, means to est. of haplotypes for
;; 'dqa1' and 'dpb1' loci followed by est. of haplotypes for 'drb1'
;; and 'dqb1' loci. A wildcard entry '*' means estimate haplotypes
;; for the entire loci as specified in the original file column order
;;lociToEstHaplo=a:b:drb1,a:b:c,drb1:dqa1:dpb1,drb1:dqb1:dpb1
lociToEstHaplo=*
;; analogous to `lociToEst' except for linkage disequilibrium (LD)
;;lociToEstLD=
;; pairwise estimates can be run in two ways: with or without
;; permutation test.
;; if LD *and* permutation test for all pairwise loci are desired,
;; then set both options '1' (true); the separate
;; 'allPairwiseLDWithHaplo' and 'allPairwiseLDWithHaploWithPermu'
;; options are now obsolete
;; estimate LD for all pairwise loci?
allPairwiseLD=1
;; with permutation test?
allPairwiseLDWithPermu=0