虽然plink2.0已经存在好久了，但是一直用的都是plink1.9，因为语法熟悉。更主要是plink2.0语法变动太大，害怕步子迈得太大了……
今天看一下plink2.0的读入和输出数据常用参数，
plink2.0用是不会用的，2022年都不会用！！！但是碰到bgen，pgen数据进行转化为bed，bim，fam文件，然后用plink1.9使用的想法还是有的，而且很大！！！
本篇目的：使用plink2.0软件将下面格式随便输入、输出
- plink1.9的ped和map数据，不如：a.ped, a.map
- plink1.9的bed和bim和fam数据，比如：a.bim, a.bed, a.fam
- plink2.0的bgen和sample数据，比如：a.bgen, a.sample
- plink2.0的pgen和bim和fam数据，比如a.pgen,a.fam,a.bim
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- vcf数据，比如a.vcf
1，plink2.0的提升
plink2.0主要是从以下几个方面，相对于plink1.9有较大的提升：
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1，保留参考等位基因的信息，比如vcf格式的数据，不要添加参数 –keep-allele-order。这样vcf变为plink，plink变为vcf就可以不用指定ref和alt了，切换无障碍！
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2，新的.pgen文件，结合SNPack-style的压缩，可以节约80%的文件大小。比如1000个Genomes，比压缩的gzip文件小70%，且不丢失任何信息。压缩文件空间更小，速度更快。
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3，旧版的二进制文件（bed，bim和fam）文件，plink2.0依旧支持，输出文件包括两种：–make-bpgen 和 –make-bpfile文件。可以支持plink1.9的文件格式，无论是map和ped数据，还是bed，bim和fam格式。
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4，分析模块，进行了优化。标准的logistic回归分析失败产生NA或者无意义的结果，–glm比plink1.9的–linear速度提升1000倍。尤其是填充的剂量效应的基因型值（比如0.2,1.8这样的非整数型数据）。PCA分析汇总，增加了参数，当样本超过1万，这个参数可以不影响精度（影响不到1%），大大提升计算效率。样本量支持得更多，处理速度更快！
2，plink2.0 安装
plink2.0 网站：https://www.cog-genomics.org/plink/2.0/
二进制文件，直接执行，支持：
- Intel
- AMD
- 苹果M1
想查看一下–export的用法，可以看到主要功能：
- A，是0-1-2编码
- ped，是map和ped格式
- vcf，是vcf格式
- bgen-1.x，包括1.1, 1.2， 1.3，都是bgen格式
$ plink2 --export --helpPLINK v2.00a3.7LM AVX2 Intel (24 Oct 2022) www.cog-genomics.org/plink/2.0/(C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3--help present, ignoring other flags.--export output format(s)...> [{01 | 12}] ['bgz'] ['id-delim='char>] ['id-paste='column set descriptor>] ['include-alt'] ['omit-nonmale-y'] ['spaces'] ['vcf-dosage='field>] ['ref-first'] ['bits='#>] ['sample-v2'] Create a new fileset with all filters applied. The following output formats are supported: (actually, only A, AD, Av, bcf, bgen-1.x, haps, hapslegend, ind-major-bed, oxford, ped, tped, and vcf are implemented for now) * '23': 23andMe 4-column format. This can only be used on a single sample's data (--keep may be handy), and does not support multicharacter allele codes. * 'A': Sample-major additive (0/1/2) coding, suitable for loading from R. If you need uncounted alleles to be named in the header line, add the 'include-alt' modifier. * 'AD': Sample-major additive (0/1/2) + dominant (het=1/hom=0) coding. Also supports 'include-alt'. * 'Av': Variant-major 0/1/2. * 'beagle': Unphased per-autosome .dat and .map files, readable by early BEAGLE versions. * 'beagle-nomap': Single .beagle.dat file. * 'bgen-1.x': Oxford-format .bgen + .sample. For v1.2/v1.3, sample identifiers are stored in the .bgen (with id-delim and id-paste settings applied), and default precision is 16-bit (use the 'bits' modifier to reduce this). * 'bimbam': Regular BIMBAM format. * 'bimbam-1chr': BIMBAM format, with a two-column .pos.txt file. Does not support multiple chromosomes. * 'fastphase': Per-chromosome fastPHASE files, with .chr-chr #>.phase.inp filename extensions. * 'fastphase-1chr': Single .phase.inp file. Does not support multiple chromosomes. * 'haps', 'hapslegend': Oxford-format .haps + .sample[ + .legend]. All data must be biallelic and phased. When the 'bgz' modifier is present, the .haps file is block-gzipped. * 'HV': Per-chromosome Haploview files, with .chr-chr #>{.ped,.info} filename extensions. * 'HV-1chr': Single Haploview .ped + .info file pair. Does not supportmultiple chromosomes. * 'ind-major-bed': PLINK 1 sample-major .bed (+ .bim + .fam). * 'lgen': PLINK 1 long-format (.lgen + .fam + .map), loadable with --lfile. * 'lgen-ref': .lgen + .fam + .map + .ref, loadable with --lfile + --reference. * 'list': Single genotype-based list, up to 4 lines per variant. To omit nonmale genotypes on the Y chromosome, add the 'omit-nonmale-y' modifier. * 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a genotype-based list which omits the most common genotype for each variant. Also supports 'omit-nonmale-y'. * 'oxford', 'oxford-v2': Oxford-format .gen + .sample. When the 'bgz' modifier is present, the .gen file is block-gzipped. 'oxford' requests the original .gen file format with 5 leading columns (understood by older PLINK builds); 'oxford-v2' requests the current 6-leading-column flavor. * 'ped', 'compound-genotypes': PLINK 1 sample-major (.ped + .map), loadable with --pedmap. * 'structure': Structure-format. * 'tped': PLINK 1 variant-major (.tped + .tfam), loadable with --tfile. * 'vcf', : VCF (default version 4.3). If PAR1 and PAR2 are present, 'vcf-4.2', they are automatically merged with chrX, with proper 'bcf', handling of chromosome codes and male ploidy. 'bcf-4.2' When the 'bgz' modifier is present, the VCF file is block-gzipped. (This always happens with BCF output.) The 'id-paste' modifier controls which .psam columns are used to construct sample IDs (choices are maybefid, fid, iid, maybesid, and sid; default is maybefid,iid,maybesid), while the 'id-delim' modifier sets the character between the ID pieces (default '_'). Genotypes are always exported来源：育种数据分析之放飞自我
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