A gen/sample pair of data files that contains a combination of GLs and fixed genotypes. All genotypes with beagle4 posteriors above a speficied threshold are fixed. And all genotypes that aren't nevertheless have GLs as enter data onto which SHAPEIT will work.
This information established also ought to be phased as properly as you can, so it is necessary to benefit from any beneficial Qualities of the information, which include significant sample measurements or family members relationships. The scaffold equivalent to the example facts established are available in scaffold.haps.gz and scaffold.haps.sample.
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-T 8 This command line can have extactly precisely the same conduct since the earlier one. Take note that in the remainder of the documentation, We're going to use this compact sort when attainable.
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SHAPEIT would not take into consideration uncertainty from the genotypes. Rather, it fixes the genotypes when their optimum chance exceeds a provided threshold and leaves as missing the Other people.
Monomorphic internet sites in PLINK Mattress format information Do not now hold the alternate allele coded as 0, which implies some incompatibility with Impute2.
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This file must have L strains where L is the volume of SNPs inside the dataset. Each and every SNP will need to have a unique physical posture. Each of the SNPs need to be purchased by Actual physical place. FAM file
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