plink1.9的GWAS数据处理流程.docxVIP

Data managementGenerate binary fileset--make-bed--make-bed?creates a new?PLINK 1 binary fileset,?after?applying sample/variant filters and other operations below. For example,plink --file?text_fileset?--maf?0.05?--make-bed --out?binary_filesetdoes the following:Autogenerate?binary_fileset-temporary.bed?+?.bim?+?.fam. (The MAF filter has not yet been applied at this stage. See the?Order of operations?page for more details.)Read?binary_fileset-temporary.bed?+?.bim?+?.fam. Calculate MAFs. Remove all variants with MAF ?0.05?from the current analysis.Generate?binary_fileset.bed?+?.bim?+?.fam. Any samples/variants removed from the current analysis are also not present in this fileset. (This is the --make-bed step.)Delete?binary_fileset-temporary.bed?+?.bim?+?.fam.In contrast, the fileset left behind by?--keep-autoconv?is just the result of step 1.--make-just-bim--make-just-fam--make-just-bim?is a variant of --make-bed which only generates a .bim file, and?--make-just-fam?plays the same role for .fam files. Unlike most other PLINK commands, these do not require the main input to include a .bed file (though you wont have access to many filtering flags when using these in no-.bed mode).Use these cautiously.?It is very easy to desynchronize your binary genotype data and your .bim/.fam indexes if you use these commands improperly. If you have any doubt, stick with --make-bed.Generate text fileset--recode 01 | 12 23 | A | A-transpose | AD | beagle | beagle-nomap | bimbam | bimbam-1chr | compound-genotypes | fastphase | fastphase-1chr | HV | HV-1chr | lgen | lgen-ref | list | oxford | rlist | structure | transpose | vcf | vcf-fid | vcf-iid tab | tabx | spacex | bgz | gen-gz include-alt omit-nonmale-y--recode-allele [filename]--recode?creates a new text fileset, after applying sample/variant filters and other operations. By default, the fileset includes a?.ped?and a?.map?file, readable with?--file.The 12 modifier causes A1 (usually minor) alleles to be coded as 1 and A2 alleles t