Warning: 225 het. haploid genotypes present (see test.hh ) 产生原因

 

001、

（1）、23号染色体

（2）、雄性

（3）、基因型为杂合

以上三个原因造成出现plink.hh文件的出现。

 

i、测试染色体。

1、

root@DESKTOP-1N42TVH:/home/test4# ls
chr23.map  chr23.ped
root@DESKTOP-1N42TVH:/home/test4# plink --file chr23 --recode --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 chr23
  --out test
  --recode

16007 MB RAM detected; reserving 8003 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (33574 variants, 165 people).
--file: test-temporary.bed + test-temporary.bim + test-temporary.fam written.
33574 variants loaded from .bim file.
165 people (80 males, 85 females) loaded from .fam.
112 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 112 founders and 53 nonfounders present.
Calculating allele frequencies... done.
Warning: 225 het. haploid genotypes present (see test.hh ); many commands treat
these as missing.
Total genotyping rate is 0.989586.
33574 variants and 165 people pass filters and QC.
Among remaining phenotypes, 56 are cases and 56 are controls.  (53 phenotypes
are missing.)
--recode ped to test.ped + test.map ... done.

 

2、改为1号染色体

root@DESKTOP-1N42TVH:/home/test4# ls
chr23.map  chr23.ped
root@DESKTOP-1N42TVH:/home/test4# awk '{OFS = "\t"; $1 = 1; print $0}' chr23.map > chr1.map
root@DESKTOP-1N42TVH:/home/test4# cp chr23.ped chr1.ped
root@DESKTOP-1N42TVH:/home/test4# ls
chr1.map  chr1.ped  chr23.map  chr23.ped
root@DESKTOP-1N42TVH:/home/test4# plink --file chr1 --recode --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 chr1
  --out test
  --recode

16007 MB RAM detected; reserving 8003 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (33574 variants, 165 people).
--file: test-temporary.bed + test-temporary.bim + test-temporary.fam written.
33574 variants loaded from .bim file.
165 people (80 males, 85 females) loaded from .fam.
112 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 112 founders and 53 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.989586.
33574 variants and 165 people pass filters and QC.
Among remaining phenotypes, 56 are cases and 56 are controls.  (53 phenotypes
are missing.)
--recode ped to test.ped + test.map ... done.

 

ii、测试性别

性别全部改为female

root@DESKTOP-1N42TVH:/home/test4# ls
chr23.map  chr23.ped
root@DESKTOP-1N42TVH:/home/test4# awk '{$5 = 2; print $0}' chr23.ped > female.ped
root@DESKTOP-1N42TVH:/home/test4# cp chr23.map female.map
root@DESKTOP-1N42TVH:/home/test4# plink --file female --recode --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 female
  --out test
  --recode

16007 MB RAM detected; reserving 8003 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (33574 variants, 165 people).
--file: test-temporary.bed + test-temporary.bim + test-temporary.fam written.
33574 variants loaded from .bim file.
165 people (0 males, 165 females) loaded from .fam.
112 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 112 founders and 53 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.989586.
33574 variants and 165 people pass filters and QC.
Among remaining phenotypes, 56 are cases and 56 are controls.  (53 phenotypes
are missing.)
--recode ped to test.ped + test.map ... done.

 

iii、测试基因型

异常个体基因型全部改为缺失或者纯合。

root@DESKTOP-1N42TVH:/home/test4# plink --file chr23 --recode --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 chr23
  --out test
  --recode

16007 MB RAM detected; reserving 8003 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (33574 variants, 165 people).
--file: test-temporary.bed + test-temporary.bim + test-temporary.fam written.
33574 variants loaded from .bim file.
165 people (80 males, 85 females) loaded from .fam.
112 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 112 founders and 53 nonfounders present.
Calculating allele frequencies... done.
Warning: 225 het. haploid genotypes present (see test.hh ); many commands treat
these as missing.
Total genotyping rate is 0.989586.
33574 variants and 165 people pass filters and QC.
Among remaining phenotypes, 56 are cases and 56 are controls.  (53 phenotypes
are missing.)
--recode ped to test.ped + test.map ... done.
root@DESKTOP-1N42TVH:/home/test4# ls
chr23.map  chr23.ped  test.hh  test.log  test.map  test.ped
root@DESKTOP-1N42TVH:/home/test4# head test.hh
1355    NA12413 rs2034740
1355    NA12413 rs6641142
1355    NA12413 rs7059273
1355    NA12413 rs1482812
1420    NA12003 rs12387774
1416    NA12248 rs7063317
1424    NA11930 rs5935527
1416    NA12248 rs5935527
1424    NA11930 rs17306502
1416    NA12248 rs17306502
root@DESKTOP-1N42TVH:/home/test4# cut -f 1 test.hh | sort | uniq | while read i; do sed -i "/^$i/ s/[ATCG]/0/g" test.ped ; done
root@DESKTOP-1N42TVH:/home/test4# ls
chr23.map  chr23.ped  test.hh  test.log  test.map  test.ped
root@DESKTOP-1N42TVH:/home/test4# plink --file test --recode --out test2
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 test2.log.
Options in effect:
  --file test
  --out test2
  --recode

16007 MB RAM detected; reserving 8003 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (33574 variants, 165 people).
--file: test2-temporary.bed + test2-temporary.bim + test2-temporary.fam
written.
33574 variants loaded from .bim file.
165 people (80 males, 85 females) loaded from .fam.
112 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 112 founders and 53 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.302329.
33574 variants and 165 people pass filters and QC.
Among remaining phenotypes, 56 are cases and 56 are controls.  (53 phenotypes
are missing.)
--recode ped to test2.ped + test2.map ... done.