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plink2.0和plink1.9的憂傷筆記

雖然plink2.0已經存在好久了，但是一直用的都是plink1.9，因為文法熟悉。更主要是plink2.0文法變動太大，害怕步子邁得太大了……

今天看一下plink2.0的讀入和輸出資料常用參數，

plink2.0用是不會用的，2022年都不會用！！！但是碰到bgen，pgen資料進行轉化為bed，bim，fam檔案，然後用plink1.9使用的想法還是有的，而且很大！！！

本篇目的：使用plink2.0軟體将下面格式随便輸入、輸出

  • plink1.9的ped和map資料，不如：a.ped, a.map
  • plink1.9的bed和bim和fam資料，比如：a.bim, a.bed, a.fam
  • plink2.0的bgen和sample資料，比如：a.bgen, a.sample
  • plink2.0的pgen和bim和fam資料，比如a.pgen,a.fam,a.bim
  • vcf資料，比如a.vcf

1，plink2.0的提升

plink2.0主要是從以下幾個方面，相對于plink1.9有較大的提升：

  • 1，保留參考等位基因的資訊，比如vcf格式的資料，不要添加參數 --keep-allele-order。這樣vcf變為plink，plink變為vcf就可以不用指定ref和alt了，切換無障礙！
  • 2，新的.pgen檔案，結合SNPack-style的壓縮，可以節約80%的檔案大小。比如1000個Genomes，比壓縮的gzip檔案小70%，且不丢失任何資訊。壓縮檔案空間更小，速度更快。
  • 3，舊版的二進制檔案（bed，bim和fam）檔案，plink2.0依舊支援，輸出檔案包括兩種：–make-bpgen 和 --make-bpfile檔案。可以支援plink1.9的檔案格式，無論是map和ped資料，還是bed，bim和fam格式。
  • 4，分析子產品，進行了優化。标準的logistic回歸分析失敗産生NA或者無意義的結果，–glm比plink1.9的–linear速度提升1000倍。尤其是填充的劑量效應的基因型值（比如0.2,1.8這樣的非整數型資料）。PCA分析彙總，增加了參數​

    ​PCA approx​

     ​，當樣本超過1萬，這個參數可以不影響精度（影響不到1%），大大提升計算效率。樣本量支援得更多，處理速度更快！

2，plink2.0 安裝

plink2.0 網站：https://www.cog-genomics.org/plink/2.0/

二進制檔案，直接執行，支援：

  • Intel
  • AMD
  • 蘋果M1
plink2.0和plink1.9的憂傷筆記

建議：plink1.9簡寫為plink，plink2.0 簡寫為plink2

3，plink幫助文檔

可以通過官網查詢具體參數：https://www.cog-genomics.org/plink/2.0/

也可以在指令行中調出幫助文檔：

比如直接鍵入plink2，出現基礎參數：

$ plink2



PLINK 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

  plink2 <input flag(s)...> [command flag(s)...] [other flag(s)...]
  plink2 --help [flag name(s)...]

Commands include --rm-dup list, --make-bpgen, --export, --freq, --geno-counts,
--sample-counts, --missing, --hardy, --het, --fst, --indep-pairwise, --ld,
--sample-diff, --make-king, --king-cutoff, --pmerge, --pgen-diff,
--write-samples, --write-snplist, --make-grm-list, --pca, --glm, --adjust-file,
--score, --variant-score, --genotyping-rate, --pgen-info, --validate, and
--zst-decompress.

"plink2 --help | more" describes all functions.

想檢視一下–export的用法，可以看到主要功能：

  • A，是0-1-2編碼
  • 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 --help
PLINK 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 support
               multiple 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.  If you want to export a
                 sites-only VCF instead, see --make-pgen/--make-just-pvar's
                 'vcfheader' column set.
                 Dosages are not exported unless the 'vcf-dosage=' modifier
                 is present.  The following six dosage export modes are
                 supported:
                 'GP': genotype posterior probabilities (v4.3 only).
                 'DS': Minimac3-style dosages, omitted for hardcalls.
                 'DS-force': Minimac3-style dosages, never omit.
                 'DS-only': Same as DS-force, except GT field is omitted.
                 'HDS': Minimac3-style phased dosages, omitted for hardcalls
                        and unphased calls.  Also includes 'DS' output.
                 'HDS-force': Always report DS and HDS.
  In addition,
  * The '12' modifier causes alt1 alleles to be coded as '1' and ref alleles
    to be coded as '2', while '01' maps alt1 -> 0 and ref -> 1.
  * The 'spaces' modifier makes the output space-delimited instead of
    tab-delimited, whenever both are permitted.
  * For biallelic formats where it's unspecified whether the reference/major
    allele should appear first or second, --export defaults to second for
    compatibility with PLINK 1.9.  Use 'ref-first' to change this.
    (Note that this doesn't apply to the 'A', 'AD', and 'Av' formats; use
    --export-allele to control which alleles are counted there.)
  * 'sample-v2' exports .sample files according to the QCTOOLv2 rather than
    the original specification.  Only one ID column is exported ('id-paste'
    and 'id-delim' settings apply), parental IDs are exported if present, and
    category names are preserved rather than converted to positive integers.

--export-allele <file> : With --export A/AD/Av, count alleles named in the
                         file, instead of REF alleles.

4. plink2.0 筆記

4.1 讀取plink的ped和map資料

plink2.0，沒有–file這個參數了，變為了：​

​--pedmap​

​，也可以分開寫，比如 --ped --map分别接ped和map資料。

plink2 --ped yuanshi.ped --map yuanshi.map

或者寫為：

plink2 --pedmap yuanshi

預設輸出檔案：

plink2.log  plink2.pgen  plink2.psam  plink2.pvar
  • plink2.log，log日志，不用理會
  • plink2.pgen，二進制檔案，類似plink1.9的bim檔案
  • plink2.psam，個體和性别資訊
  • plink2.pvar，snp的資訊，包括染色體、實體位置、名稱、ref和alt

4.2 讀取plink的bed，bim和fam資料

plink1.9的二進制資料是bed，bim和fam資料，plink2.0通過–bfile指定。

比如讀取plink1.9的二進制檔案，輸出bgen格式：

plink2 --bfile a1 --export bgen-1.1 --out t1

日志：

$ plink2 --bfile a1 --export bgen-1.1 --out t1
PLINK 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
Logging to t1.log.
Options in effect:
  --bfile a1
  --export bgen-1.1
  --out t1

Start time: Thu Dec  1 18:59:10 2022
1031523 MiB RAM detected; reserving 515761 MiB for main workspace.
Using up to 96 threads (change this with --threads).
86 samples (0 females, 0 males, 86 ambiguous; 86 founders) loaded from a1.fam.
50904 variants loaded from a1.bim.
Note: No phenotype data present.
Writing t1.bgen ... done.
Writing t1.sample ... done.

4.3 讀取bgen和sample格式

導出ped和map的格式：

plink2 --bgen t1.bgen 'ref-last' --sample t1.sample --export ped --out x1

注意：bgen和sample是一對資料，讀取時，要分開指定，–bgen， --sample，同時要指定‘ref-last’，即後面的是ref，前面的是alt，也可以修改。

4.4 讀取vcf資料

導出ped和map資料

讀取vcf，導出ped和map資料：需要定義​

​--export ped​

​

plink2 --vcf x2.vcf --export ped --out y1

導出bed和bim和fam資料

讀取vcf資料，導出bim，bed和fam資料：需要定義​

​--make-bed​

​

plink2 --vcf x2.vcf --make-bed --out y2

導出bgen資料

plink2 --vcf x2.vcf --export bgen-1.1 --out y3
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