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The --hapmap option is now deprecated. Please use --haps instead. If you have a different requirement, you can always specify --hapmap-file .
PLINK 2 can be used with input files that contain chromosome-specific regions. Sample major (i.e. group-based) and minor (i.e. variant-based) genotypes for the same individual can be stored in parallel in separate data files, and the major and minor genotype sets can be combined at the end. This is especially useful if, for example, you need to merge large numbers of 1000 Genomes samples.
PLINK 2's new variant-based genotyping by locus (VGL) functionality can be used to detect and optionally remove known pseudogenes and other non-functional variants. This functionality is disabled by default. If you have a list of known pseudogenes, you can use --remove-hapmap to specify a list of variants to remove. To remove all pseudogenes in a dataset, use --remove-hapmap --remove-hapmap-file .
--geno lets you specify which are the SNPs to use for generating the genotype frequencies. PLINK 2 will not attempt to correct for missing genotypes, and will assume that all genotypes are present. This is a convenient way to generate files for a subset of the PLINK input. (It is not possible to specify more than one --geno flag at the same time.) The following values are understood:
--alt-hwe allows the user to specify either a variant or a file containing a list of variants, and causes PLINK 2 to interpret the variants in the file as homozygous reference sites. Note that PLINK 2 requires that the variants in the.sample file be explicitly specified and that no duplicate variants are present.
--cmdline allows the command-line options to be specified in a file. The file should be a list of all the options delimited by newlines (the option --cmdline-delim can be used to specify different delimiters).
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