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1、Data man ageme ntGen erate binary fileset-make - bed-make-b ed creates a new PLINK 1 bi nary fileset , after appl ying sample/varia nt filters and other operations below. For example,pli nk -filetext_fileset -maf 0.05 -make-b ed -out bin ary_filesetdoes the follow ing:1. Autogenerate binary_fileset-
2、temporary.bed + .bim + .fam . (TheMAF filter has not yet bee n applied at this stage. See the Order of operations page for more details.)2. Read binary_fileset -temporary.bed + .bim + .fam . CalculateMAFs. Remove all varia nts with MAF 0.05 from the curre nt an alysis.3. Gen erate bin ary_fileset.be
3、d + .bim + .fam . Any samples/varia ntsremoved from the current analysis are also not present in this fileset. (Thisis the -make-bed step.)4. 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-jus
4、t-fam-make-just-bim is a varia nt of -make - bed which only gen erates a .bim file, and -make-just-fam plays the same role for .fam files. Un like most other PLINK comma nds, these do not require the main in put to in clude a .bed file (though you wont have access to many filtering flags when using
5、these in no-.bed mode).Use these cautiously. It is very easy to des ynchronize your binary geno type data and your .bim/.fam in dexes if you use these comma nds improperly. If you have any doubt, stick with -make-bed.Gen erate text fileset-recode vin clude-alt -recode-allele file name-recode creates
6、 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 andA2 alleles to be coded as 2, while 01 maps A1 f 0 and A2 f 1. (PLINKfo
7、rces you to combine 01 with-output-missing-genotype when this isnecessary to prevent missing genotypes from becoming indistinguishable from A1 calls.)? The 23 modifier causes a 23andMe-formatted file to be generated. This can only be used on a single samples data (a one-line-keep file maycome in han
8、dy here). There is currently no special handling of the XY pseudo-autosomal region.? The AD modifier causes an additive (0/1/2) + dominant (het = 1, otherwise 0) component file , suitable for loading from R, to be generated. A is the same, except without the dominance component.o By default, A1 alle
9、les are counted; this can be customized with -recode-allele . -recode-alleles input file should have variant IDs in the first column and allele IDs in the second.o By default, the header line for .raw files only names the counted alleles. To include the alternate allele codes as well, add the includ
10、e-alt modifier.o Haploid additive components are 0/2-valued instead of 0/1-valued, to maintain a consistent scale on the X chromosome.See also -R.The A-transpose modifier causes a variant-major additive component file to be generated. This can also be used with -recode-allele.The beagle modifier cau
11、ses unphased per-autosome .dat and .map files, readable by BEAGLE 3.3 and earlier, to be generated, while beagle- nomap generates a single .dat file (no chromosome splitting occurs in this case).The bimbam modifier causes a BIMBAM-formatted fileset to be generated. If your input data only contains o
12、ne chromosome, you can use bimbam-1chr instead to write a two-column .pos.txt file.If all allele codes are single-character, you can use the compoundgenotypes modifier to omit the space between each pair of allele codes in a single genotype call when generating a .ped + .map fileset. You will need t
13、o use the -compound-genotypes flag to load this data in PLINK 1.07, but its not needed for PLINK 1.9.The fastphase modifier causes per-chromosome fastPHASE files to be generated. If your input data only contains one chromosome, you can usefastphase-1chr instead to exclude the chromosome number from
14、the file extension.The HV modifier causes a Haploview-format .ped + .info fileset to be generated per chromosome. HV-1chr is analogous to fastphase-1chr.The lgen modifier causes a long-format fileset , loadable with -lfile , to be generated. lgen-ref is equivalent to PLINK 1.07 -recode-lgen -with- reference.The list modifier causes a genotype-based list to be generated. This does not produce a .fam or .map file.The oxford modifier causes a Oxford-format .gen + .sample fileset to be generated. If you also include the gen-gz modifier, the .gen file is gzipped.The rlist modifier
