Attachment 318020 Details for Bug 464460 – sample.ini (configuration file)

sample.ini (configuration file)

sample.ini (text/plain), 1.51 KB, created by Alex Lancaster on 2008-09-29 22:54:14 UTC

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Creator: Alex Lancaster

Created: 2008-09-29 22:54:14 UTC

Size: 1.51 KB

patch

obsolete

>;; comment out or change as desired
>;; 1 = true, 0 = false
>
>[General]
>debug=0
>
>[ParseGenotypeFile]
>untypedAllele=****
>
>;; designates field name that holds allele data
>alleleDesignator=*
>
>;; valid fields for sample data block
>validSampleFields=*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
>
>[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
>
>;; 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

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Attachments on bug 464460: 318020 | 318021 | 318022