plink2.0和plink1.9的忧伤笔记

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
• • 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：

• 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！

• 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。

• 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。

• 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 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
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