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This allows for the 0, 1, 2 count to reflect the number of a pre-specified allele type per SNP, rather than the number of the minor allele.This command takes as a single argument the name of a file that lists SNP name and allele to report, e.g.The order of individuals in this file is the same as the order across the columns of the TPED file.

Unless manually specified, for all these options, the usual filters for missingness and allele frequency will be set so as not to exclude any SNPs or individuals. Alleles other than A, C, G, T or 1,2,3,4 will be left unchanged.It is sometimes useful to have a PED file that is tab-delimited, except that between alleles of the same genotype a space instead of a tab is used.Introduction | Basics | Download | Reference | Formats | Data management | Summary stats | Filters | Stratification | IBS/IBD | Association | Family-based | Permutation | LD calcualtions | Haplotypes | Conditional tests | Proxy association | Imputation | Dosage data | Meta-analysis | Result annotation | Clumping | Gene Report | Epistasis | Rare CNVs | Common CNPs | R-plugins | SNP annotation | Simulation | Profiles | ID helper | Resources | Flow chart | Misc.| FAQ | g PLINK (where, as usual, "plink" would be replaced by any specified --out {filename} ). to invole an evalation of Mendel errors, which does not occur by default, by not excluding any individuals or SNPs based on the results, i.e. To recode SNP alleles from A, C, G, T to 1,2,3,4 or vice versa, use ), or any other analysis or summary statistic option.The following format is often useful if one wants to use a standard, non-genetic statistical package to analyse the data, as here genotypes are coded as a single allele dosage number.

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To create a file with SNP genotypes recoded in terms of additive and dominant components, use the option: which, assuming command.

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