plink 软件中 --het参数

 

001、

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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
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002、F来源：https://www.cog-genomics.org/plink/1.9/basic_stats#ibc

 

 

003、验证：

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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
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004、 O(HOM)、E(HOM)、N(NM)如何计算

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root@DESKTOP-1N42TVH:/home/test5# ls
verify.map  verify.ped
root@DESKTOP-1N42TVH:/home/test5# cat verify.map
1       s64199.1        0       55910
1       OAR19_64675012.1        0       85204
1       OAR19_64715327.1        0       122948
1       OAR19_64803054.1        0       203750
1       DU281551_498.1  0       312707
1       s18939.1        0       356863
1       OAR1_88143.1    0       400518
1       s09912.1        0       487423
root@DESKTOP-1N42TVH:/home/test5# cat verify.ped
DOR     1       0       0       0       -9      G G     C C     T G     G G     A G     A C     G G     G C
DOR     2       0       0       0       -9      C C     G C     T G     G G     G G     A C     A G     C C
DOR     3       0       0       0       -9      G G     C C     T T     G G     G G     A A     A G     G C
DOR     4       0       0       0       -9      G G     C C     G G     G G     G G     A A     G G     G G
DOR     5       0       0       0       -9      G G     C C     G G     G G     G G     A A     A G     G C
DOR     6       0       0       0       -9      G G     C C     G G     G G     G G     A A     A A     C C
DOR     7       0       0       0       -9      G G     C C     G G     A G     A A     A A     G G     C C
DOR     9       0       0       0       -9      G G     C C     G G     A G     A A     A A     G G     C C
DOR     10      0       0       0       -9      G G     G C     G G     G G     G G     A A     A G     C C
DOR     11      0       0       0       -9      G G     C C     G G     G G     A G     C C     A G     G C
root@DESKTOP-1N42TVH:/home/test5# plink --file verify --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 verify
  --het
  --out test

16007 MB RAM detected; reserving 8003 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (8 variants, 10 people).
--file: test-temporary.bed + test-temporary.bim + test-temporary.fam written.
8 variants loaded from .bim file.
10 people (0 males, 0 females, 10 ambiguous) loaded from .fam.
Ambiguous sex IDs written to test.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 10 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is exactly 1.
8 variants and 10 people pass filters and QC.
Note: No phenotypes present.
--het: 8 variants scanned, report written to test.het .
root@DESKTOP-1N42TVH:/home/test5# ls
test.het  test.log  test.nosex  verify.map  verify.ped
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root@DESKTOP-1N42TVH:/home/test5# ls
test.het  test.log  test.nosex  verify.map  verify.ped
root@DESKTOP-1N42TVH:/home/test5# cat test.het
 FID  IID       O(HOM)       E(HOM)        N(NM)            F
 DOR    1            4        5.525            8      -0.6162
 DOR    2            4        5.525            8      -0.6162
 DOR    3            6        5.525            8       0.1919
 DOR    4            8        5.525            8            1
 DOR    5            6        5.525            8       0.1919
 DOR    6            8        5.525            8            1
 DOR    7            7        5.525            8        0.596
 DOR    9            7        5.525            8        0.596
 DOR   10            6        5.525            8       0.1919
 DOR   11            5        5.525            8      -0.2121
root@DESKTOP-1N42TVH:/home/test5# cat verify.ped
DOR     1       0       0       0       -9      G G     C C     T G     G G     A G     A C     G G     G C
DOR     2       0       0       0       -9      C C     G C     T G     G G     G G     A C     A G     C C
DOR     3       0       0       0       -9      G G     C C     T T     G G     G G     A A     A G     G C
DOR     4       0       0       0       -9      G G     C C     G G     G G     G G     A A     G G     G G
DOR     5       0       0       0       -9      G G     C C     G G     G G     G G     A A     A G     G C
DOR     6       0       0       0       -9      G G     C C     G G     G G     G G     A A     A A     C C
DOR     7       0       0       0       -9      G G     C C     G G     A G     A A     A A     G G     C C
DOR     9       0       0       0       -9      G G     C C     G G     A G     A A     A A     G G     C C
DOR     10      0       0       0       -9      G G     G C     G G     G G     G G     A A     A G     C C
DOR     11      0       0       0       -9      G G     C C     G G     G G     A G     C C     A G     G C
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 个体期待纯合度：E(HOM) 如何计算？

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root@DESKTOP-1N42TVH:/home/test5# ls
test.het  test.log  test.nosex  verify.map  verify.ped
root@DESKTOP-1N42TVH:/home/test5# plink --file verify --hardy --out hardy
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 hardy.log.
Options in effect:
  --file verify
  --hardy
  --out hardy

16007 MB RAM detected; reserving 8003 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (8 variants, 10 people).
--file: hardy-temporary.bed + hardy-temporary.bim + hardy-temporary.fam
written.
8 variants loaded from .bim file.
10 people (0 males, 0 females, 10 ambiguous) loaded from .fam.
Ambiguous sex IDs written to hardy.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 10 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is exactly 1.
--hardy: Writing Hardy-Weinberg report (founders only) to hardy.hwe ... done.
root@DESKTOP-1N42TVH:/home/test5# ls
hardy.hwe  hardy.log  hardy.nosex  test.het  test.log  test.nosex  verify.map  verify.ped
root@DESKTOP-1N42TVH:/home/test5# cat hardy.hwe   ## 倒数第二列，位点的期待杂合度， 由此可计算期待纯合度，所有位点期待纯合度累加， 获取个体期待纯合度
 CHR                SNP     TEST   A1   A2                 GENO   O(HET)   E(HET)            P
   1           s64199.1  ALL(NP)    C    G                1/0/9        0     0.18      0.05263
   1   OAR19_64675012.1  ALL(NP)    G    C                0/2/8      0.2     0.18            1
   1   OAR19_64715327.1  ALL(NP)    T    G                1/2/7      0.2     0.32       0.3065
   1   OAR19_64803054.1  ALL(NP)    A    G                0/2/8      0.2     0.18            1
   1     DU281551_498.1  ALL(NP)    A    G                2/2/6      0.2     0.42       0.1331
   1           s18939.1  ALL(NP)    C    A                1/2/7      0.2     0.32       0.3065
   1       OAR1_88143.1  ALL(NP)    A    G                1/5/4      0.5    0.455            1
   1           s09912.1  ALL(NP)    G    C                1/4/5      0.4     0.42            1
root@DESKTOP-1N42TVH:/home/test5# ls
hardy.hwe  hardy.log  hardy.nosex  test.het  test.log  test.nosex  verify.map  verify.ped
root@DESKTOP-1N42TVH:/home/test5# cat hardy.hwe
 CHR                SNP     TEST   A1   A2                 GENO   O(HET)   E(HET)            P
   1           s64199.1  ALL(NP)    C    G                1/0/9        0     0.18      0.05263
   1   OAR19_64675012.1  ALL(NP)    G    C                0/2/8      0.2     0.18            1
   1   OAR19_64715327.1  ALL(NP)    T    G                1/2/7      0.2     0.32       0.3065
   1   OAR19_64803054.1  ALL(NP)    A    G                0/2/8      0.2     0.18            1
   1     DU281551_498.1  ALL(NP)    A    G                2/2/6      0.2     0.42       0.1331
   1           s18939.1  ALL(NP)    C    A                1/2/7      0.2     0.32       0.3065
   1       OAR1_88143.1  ALL(NP)    A    G                1/5/4      0.5    0.455            1
   1           s09912.1  ALL(NP)    G    C                1/4/5      0.4     0.42            1
root@DESKTOP-1N42TVH:/home/test5# sed 1d hardy.hwe
   1           s64199.1  ALL(NP)    C    G                1/0/9        0     0.18      0.05263
   1   OAR19_64675012.1  ALL(NP)    G    C                0/2/8      0.2     0.18            1
   1   OAR19_64715327.1  ALL(NP)    T    G                1/2/7      0.2     0.32       0.3065
   1   OAR19_64803054.1  ALL(NP)    A    G                0/2/8      0.2     0.18            1
   1     DU281551_498.1  ALL(NP)    A    G                2/2/6      0.2     0.42       0.1331
   1           s18939.1  ALL(NP)    C    A                1/2/7      0.2     0.32       0.3065
   1       OAR1_88143.1  ALL(NP)    A    G                1/5/4      0.5    0.455            1
   1           s09912.1  ALL(NP)    G    C                1/4/5      0.4     0.42            1
root@DESKTOP-1N42TVH:/home/test5# sed 1d hardy.hwe | awk 'BEGIN {sum = 0} {sum += (1 - $(NF - 1))} END {print sum}'
5.525
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posted @   小鲨鱼2018  阅读(897)  评论(0)  编辑  收藏  举报
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