Beta 2 build posted
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Christopher Chang
Jul 3, 2014, 5:50:41 AM7/3/14
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Beta 2 is now posted. In addition to bugfixes, this includes:
* --dosage.
* family-based quantitative trait association tests (--qfam...).
* --indep-pairphase, which uses maximum likelihood pairwise phasing instead of allele count correlations for LD-based pruning. (This isn't actually much better than --indep-pairwise, but it also isn't much slower.)
* a basic Wright's Fst calculation (--fst).
* --oxford-pheno-name, to select the phenotype to import from a .sample file.
* Cochran-Mantel-Haenszel stratified case/control tests.
* --dosage.
* family-based quantitative trait association tests (--qfam...).
* --indep-pairphase, which uses maximum likelihood pairwise phasing instead of allele count correlations for LD-based pruning. (This isn't actually much better than --indep-pairwise, but it also isn't much slower.)
* a basic Wright's Fst calculation (--fst).
* --oxford-pheno-name, to select the phenotype to import from a .sample file.
* Cochran-Mantel-Haenszel stratified case/control tests.
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