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.
