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SAS features a crucial programming feature known as macros that permit you to execute the repetitive areas of the code and use this macro, again and again, to complete a similar task yet again Down the road. This helps you to generate several dynamic variables during the code that can choose different values for various cases to operate a similar code. You can even declare macros for some code blocks, which you'll reuse later any quantity of instances comparable to that of macro variables.

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* Insignificant: When running on ped/map documents at monomorphic SNPs the output files shown The 2 alleles since the observed allele and 0.This has now been modified so which the observed allele is outlined twice.This provides much better compatibility with IMPUTE2.

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Threshold for really hard contacting genotypes when GEN/SAMPLE documents are supplied as enter. For every individual at Each and every SNP, the program will assume that the probably genotype is correct if its chance exceeds the brink.

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To begin with, all of the samples are phased ignoring the pedigree info. This phasing is incredibly correct In spite of not utilizing the pedigree details. The key reason why would be that the sharing of long-array haplotypes concerning connected samples in fact helps the phasing throughout the MCMC algorithm that SHAPEIT implements. Secondly, Now look at here now we have created a fresh method (called duoHMM) that takes the estimated haplotype from the first step, and brings together it While using the identified pedigree details to why not find out more even more Increase the phasing. This method important link will make certain that the haplotypes are in line with the pedigree framework, bringing about greater accuracy.

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It is possible to alter the number of threads that SHAPEIT works by using. This selection was made to speed up SHAPEIT when operating on multi-core pcs. For instance, Should you have a four-Main Laptop or computer, Then you can certainly run the following command: shapeit -B gwas

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