![]() By default, A1 alleles are counted this can be customized with -recode-allele.' A' is the same, except without the dominance component. The ' AD' modifier causes an additive (0/1/2) + dominant (het = 1, otherwise 0) component file, suitable for loading from R, to be generated.There is currently no special handling of the XY pseudo-autosomal region. This can only be used on a single sample's data (a one-line -keep file may come in handy here). The ' 23' modifier causes a 23andMe-formatted file to be generated.(PLINK forces you to combine '01' with -missing-genotype when this is necessary to prevent missing genotypes from becoming indistinguishable from A1 calls.) The ' 12' modifier causes A1 (usually minor) alleles to be coded as '1' and A2 alleles to be coded as '2', while ' 01' maps A1→0 and A2→1.recode creates a new text fileset, after applying sample/variant filters and other operations. See the Order of operations page for more details.) (The MAF filter has not yet been applied at this stage. Autogenerate binary_fileset -temporary.bed +.Plink -file text_fileset -maf 0.05 -make-bed -out binary_fileset make-bed creates a new PLINK 1 binary fileset, after applying sample/variant filters and other operations below.
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