plink 软件中 --het参数
作者：互联网
001、
root@DESKTOP-1N42TVH:/home/test4# ls outcome.map outcome.ped root@DESKTOP-1N42TVH:/home/test4# plink --file outcome --het --out test PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/ (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to test.log. Options in effect: --file outcome --het --out test 16007 MB RAM detected; reserving 8003 MB for main workspace. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (21542 variants, 20 people). --file: test-temporary.bed + test-temporary.bim + test-temporary.fam written. 21542 variants loaded from .bim file. 20 people (0 males, 0 females, 20 ambiguous) loaded from .fam. Ambiguous sex IDs written to test.nosex . Using 1 thread (no multithreaded calculations invoked). Before main variant filters, 20 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is exactly 1. 21542 variants and 20 people pass filters and QC. Note: No phenotypes present. --het: 19263 variants scanned, report written to test.het . root@DESKTOP-1N42TVH:/home/test4# ls outcome.map outcome.ped test.het test.log test.nosex root@DESKTOP-1N42TVH:/home/test4# cat test.het FID IID O(HOM) E(HOM) N(NM) F DOR 1 12374 1.257e+04 19263 -0.02885 DOR 2 13047 1.257e+04 19263 0.07166 DOR 3 11857 1.257e+04 19263 -0.1061 DOR 4 12037 1.257e+04 19263 -0.07918 DOR 5 12558 1.257e+04 19263 -0.00137 DOR 6 12152 1.257e+04 19263 -0.062 DOR 7 11860 1.257e+04 19263 -0.1056 DOR 9 12607 1.257e+04 19263 0.005948 DOR 10 11988 1.257e+04 19263 -0.0865 DOR 11 12692 1.257e+04 19263 0.01864 DOR 12 11958 1.257e+04 19263 -0.09098 DOR 13 12396 1.257e+04 19263 -0.02556 DOR 14 12080 1.257e+04 19263 -0.07276 DOR 15 11938 1.257e+04 19263 -0.09396 DOR 16 12414 1.257e+04 19263 -0.02288 DOR 17 11979 1.257e+04 19263 -0.08784 DOR 18 12288 1.257e+04 19263 -0.04169 DOR 19 12247 1.257e+04 19263 -0.04782 DOR 20 12790 1.257e+04 19263 0.03328 DOR 22 12334 1.257e+04 19263 -0.03482
002、F来源：https://www.cog-genomics.org/plink/1.9/basic_stats#ibc
003、验证：
root@DESKTOP-1N42TVH:/home/test4# ls
outcome.map outcome.ped test.het test.log test.nosex
root@DESKTOP-1N42TVH:/home/test4# cat test.het
FID IID O(HOM) E(HOM) N(NM) F
DOR 1 12374 1.257e+04 19263 -0.02885
DOR 2 13047 1.257e+04 19263 0.07166
DOR 3 11857 1.257e+04 19263 -0.1061
DOR 4 12037 1.257e+04 19263 -0.07918
DOR 5 12558 1.257e+04 19263 -0.00137
DOR 6 12152 1.257e+04 19263 -0.062
DOR 7 11860 1.257e+04 19263 -0.1056
DOR 9 12607 1.257e+04 19263 0.005948
DOR 10 11988 1.257e+04 19263 -0.0865
DOR 11 12692 1.257e+04 19263 0.01864
DOR 12 11958 1.257e+04 19263 -0.09098
DOR 13 12396 1.257e+04 19263 -0.02556
DOR 14 12080 1.257e+04 19263 -0.07276
DOR 15 11938 1.257e+04 19263 -0.09396
DOR 16 12414 1.257e+04 19263 -0.02288
DOR 17 11979 1.257e+04 19263 -0.08784
DOR 18 12288 1.257e+04 19263 -0.04169
DOR 19 12247 1.257e+04 19263 -0.04782
DOR 20 12790 1.257e+04 19263 0.03328
DOR 22 12334 1.257e+04 19263 -0.03482
root@DESKTOP-1N42TVH:/home/test4# awk 'NR != 1{print ($3 - $4)/($5 - $4)}' test.het
-0.0292843
0.0712685
-0.106529
-0.0796354
-0.00179292
-0.0624533
-0.106081
0.00552816
-0.0869565
0.018228
-0.0914388
-0.0259973
-0.0732108
-0.094427
-0.0233079
-0.0883012
-0.0421336
-0.0482594
0.0328702
-0.0352607
004、 O(HOM)、E(HOM)、N(NM)如何计算
标签：het,19263,plink,04,--,test,DOR,1.257 来源： https://www.cnblogs.com/liujiaxin2018/p/16472031.html