plink的GWAS数据处理作业流程.docx
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1、Data managementGenerate binary fileset-make-bed-make-bedcreates a newPLINK 1 binary fileset,afterapplying sample/variant filters and other operations below. For example,plink -filetext_fileset-maf0.05-make-bed -outbinary_filesetdoes the following:1. Autogeneratebinary_fileset-temporary.bed+.bim+.fam
2、. (The MAF filter has not yet been applied at this stage. See theOrder of operationspage for more details.)2. Readbinary_fileset-temporary.bed+.bim+.fam. Calculate MAFs. Remove all variants with MAF 0.05from the current analysis.3. Generatebinary_fileset.bed+.bim+.fam. Any samples/variants removed f
3、rom the current analysis are also not present in this fileset. (This is the -make-bed step.)4. Deletebinary_fileset-temporary.bed+.bim+.fam.In contrast, the fileset left behind by-keep-autoconvis just the result of step 1.-make-just-bim-make-just-fam-make-just-bimis a variant of -make-bed which only
4、 generates a .bim file, and-make-just-famplays 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 des
5、ynchronize 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 -recode-allele filename-recodecreates a new text fileset, after applying sample/variant filters and other operations. By defa
6、ult, the fileset includes a.pedand a.mapfile, readable with-file. The 12 modifier causes A1 (usually minor) alleles to be coded as 1 and A2 alleles to be coded as 2, while 01 maps A10 and A21. (PLINK forces you to combine 01 with-output-missing-genotypewhen this is necessary to prevent missing genot
7、ypes 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-keepfile may come in handy here). There is currently no special handling of the XY pseudo-autosomal region. The AD modifier
8、 causes anadditive (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 alleles are counted; this can be customized with-recode-allele. -recode-alleles input file should have var
9、iant 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 include-alt modifier.o Haploid additive components are 0/2-valued instead of 0/1-valued, to maintain a consist
10、ent scale on the X chromosome.See also-R. The A-transpose modifier causes avariant-major additive component fileto be generated. This can also be used with -recode-allele. The beagle modifier causes unphased per-autosome.dat and .mapfiles, readable byBEAGLE3.3 and earlier, to be generated, while bea
11、gle-nomap generates a single .dat file (no chromosome splitting occurs in this case). The bimbam modifier causes aBIMBAM-formatted filesetto be generated. If your input data only contains one chromosome, you can use bimbam-1chr instead to write a two-column .pos.txt file. If all allele codes are sin
12、gle-character, you can use the compound-genotypes 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 to use the -compound-genotypes flag to load this data in PLINK 1.07, but its not needed for PLINK 1.9. The fas
13、tphase modifier causes per-chromosomefastPHASE filesto be generated. If your input data only contains one chromosome, you can use fastphase-1chr instead to exclude the chromosome number from the file extension. The HV modifier causes a Haploview-format .ped +.infofileset to be generated per chromoso
14、me. HV-1chr is analogous to fastphase-1chr. The lgen modifier causes along-format fileset, loadable with-lfile, to be generated. lgen-ref is equivalent to PLINK 1.07 -recode-lgen -with-reference. The list modifier causes agenotype-based listto be generated. This does not produce a .fam or .map file.
15、 The oxford modifier causes a Oxford-format.gen+.samplefileset to be generated. If you also include the gen-gz modifier, the .gen file is gzipped. The rlist modifier causes arare-genotype filesetto be generated (similar to -lists output, but with .fam and .map files, and without homozygous major gen
16、otypes). With the list and rlist formats, the omit-nonmale-y modifier causes nonmale genotypes to be omitted on the Y chromosome. The structure modifier causes aStructure-format fileto be generated. The transpose modifier causes atransposed text fileset, loadable with-tfile, to be generated. The vcf
17、, vcf-fid, and vcf-iid modifiers result in production of aVCFv4.2 file. vcf-fid and vcf-iid cause family IDs and within-family IDs respectively to be used for the sample IDs in the last header row, while vcf merges both IDs and puts an underscore between them (in this case, a warning will be given i
18、f an ID already contains an underscore).If the bgz modifier is added, the VCF file is block-gzipped. (Gzipping of other -recode output files is not currently supported.)The A2 allele is saved as the reference and normally flagged as not based on a real reference genome (PR INFO field value). When it
19、 is important for reference alleles to be correct, youll usually also want to include-a2-allele and -real-ref-allelesin your command. The tab modifier makes the output mostly tab-delimited instead of mostly space-delimited when the format permits both delimiters. tabx and spacex force all tabs and a
20、ll spaces, respectively. (Seethis pagefor guidelines on swapping tabs/spaces in other contexts.)For example,plink -bfilebinary_fileset-recode -outnew_text_filesetgeneratesnew_text_fileset.pedandnew_text_fileset.mapfrom the data inbinary_fileset.bed+.bim+.fam, whileplink -bfilebinary_fileset-recode v
21、cf-iid -outnew_vcfgeneratesnew_vcf.vcffrom the same data, removing family IDs in the process.Irregular output coding-output-chr MT codeNormally, autosomal/sex/mitochondrial chromosome codes in PLINK output files are numeric, e.g. 23 for human X.-output-chrlets you specify a different coding scheme b
22、y providing the desired human mitochondrial code; supported options are 26 (default), M, MT, 0M, chr26, chrM, and chrMT. (PLINK 1.9 correctly interprets all of these encodings in input files.)-output-missing-genotype char-output-missing-phenotype string-output-missing-genotypeallows you to change th
23、e character (normally the-missing-genotypevalue) used to represent missing genotypes in PLINK output files, while-output-missing-phenotypechanges the string (normally the-missing-phenotypevalue) representing missing phenotypes.Note that these flags do not affect -bmerge/-merge-list or the autoconver
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