plink 软件中 --check-sex参数
作者：互联网
1、--check-sex用于验证性别信息是否可靠。 检测依据是对x染色体进行纯合度F值统计。
001、
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# ls HapMap_3_r3_5.bed HapMap_3_r3_5.bim HapMap_3_r3_5.fam ## 检测性别异常个体 root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# plink --bfile HapMap_3_r3_5 --check-sex 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 plink.log. Options in effect: --bfile HapMap_3_r3_5 --check-sex 16007 MB RAM detected; reserving 8003 MB for main workspace. 1430443 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: 179 het. haploid genotypes present (see plink.hh ); many commands treat these as missing. Total genotyping rate is 0.997899. 1430443 variants and 165 people pass filters and QC. Among remaining phenotypes, 56 are cases and 56 are controls. (53 phenotypes are missing.) --check-sex: 23424 Xchr and 0 Ychr variant(s) scanned, 1 problem detected. Report written to plink.sexcheck .
提取异常个体：
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# ls
HapMap_3_r3_5.bed HapMap_3_r3_5.bim HapMap_3_r3_5.fam plink.hh plink.log plink.sexcheck
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# head plink.sexcheck
FID IID PEDSEX SNPSEX STATUS F
1328 NA06989 2 2 OK -0.01184
1377 NA11891 1 1 OK 1
1349 NA11843 1 1 OK 1
1330 NA12341 2 2 OK -0.01252
1444 NA12739 1 1 OK 1
1344 NA10850 2 2 OK 0.01496
1328 NA06984 1 1 OK 1
1463 NA12877 1 1 OK 1
1418 NA12275 2 2 OK -0.1028
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# awk '$(NF - 1) != "OK"' plink.sexcheck
FID IID PEDSEX SNPSEX STATUS F
1349 NA10854 2 1 PROBLEM 0.99 ## 有问题的个体
002、验证
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# ls
HapMap_3_r3_5.bed HapMap_3_r3_5.bim HapMap_3_r3_5.fam
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# wc -l HapMap_3_r3_5.fam
165 HapMap_3_r3_5.fam
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# awk 'BEGIN {print 1/(165 * 2)}'
0.0030303
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# plink --bfile HapMap_3_r3_5 --chr 23 --maf 0.0030303 --recode --out chr23
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 chr23.log.
Options in effect:
--bfile HapMap_3_r3_5
--chr 23
--maf 0.0030303
--out chr23
--recode
16007 MB RAM detected; reserving 8003 MB for main workspace.
31490 out of 1430443 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: 179 het. haploid genotypes present (see chr23.hh ); many commands
treat these as missing.
Total genotyping rate is 0.990832.
8066 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
23424 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 chr23.ped + chr23.map ... done.
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# ls
HapMap_3_r3_5.bed HapMap_3_r3_5.bim HapMap_3_r3_5.fam chr23.hh chr23.log chr23.map chr23.ped
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# head chr23.map
23 rs311168 0 2720840
23 rs311173 0 2722661
23 rs311183 0 2724756
23 rs311187 0 2726346
23 rs5939329 0 2728135
23 rs3672 0 2743641
23 rs3671 0 2743668
23 rs901321 0 2747282
23 rs5982872 0 2754765
23 rs5939351 0 2760122
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# sed 's/^.//' chr23.map -i
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# head chr23.map
3 rs311168 0 2720840
3 rs311173 0 2722661
3 rs311183 0 2724756
3 rs311187 0 2726346
3 rs5939329 0 2728135
3 rs3672 0 2743641
3 rs3671 0 2743668
3 rs901321 0 2747282
3 rs5982872 0 2754765
3 rs5939351 0 2760122
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# plink --file chr23 --het --out chr23_3
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 chr23_3.log.
Options in effect:
--file chr23
--het
--out chr23_3
16007 MB RAM detected; reserving 8003 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (23424 variants, 165 people).
--file: chr23_3-temporary.bed + chr23_3-temporary.bim + chr23_3-temporary.fam
written.
23424 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 0.990283.
23424 variants and 165 people pass filters and QC.
Among remaining phenotypes, 56 are cases and 56 are controls. (53 phenotypes
are missing.)
--het: 23424 variants scanned, report written to chr23_3.het .
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# head chr23_3.het
FID IID O(HOM) E(HOM) N(NM) F
1328 NA06989 16128 1.621e+04 23373 -0.01142
1377 NA11891 23384 1.622e+04 23384 1
1349 NA11843 23412 1.624e+04 23412 1
1330 NA12341 16132 1.622e+04 23388 -0.01209
1444 NA12739 23405 1.623e+04 23405 1
1344 NA10850 16327 1.622e+04 23385 0.01538
1328 NA06984 23419 1.624e+04 23419 1
1463 NA12877 23387 1.622e+04 23387 1
1418 NA12275 15464 1.62e+04 23352 -0.1023
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# awk '{print $5}' chr23.ped | sed '1i sex' | paste - chr23_3.het | head
sex FID IID O(HOM) E(HOM) N(NM) F
2 1328 NA06989 16128 1.621e+04 23373 -0.01142 ## f值一致
1 1377 NA11891 23384 1.622e+04 23384 1
1 1349 NA11843 23412 1.624e+04 23412 1
2 1330 NA12341 16132 1.622e+04 23388 -0.01209
1 1444 NA12739 23405 1.623e+04 23405 1
2 1344 NA10850 16327 1.622e+04 23385 0.01538
1 1328 NA06984 23419 1.624e+04 23419 1
1 1463 NA12877 23387 1.622e+04 23387 1
2 1418 NA12275 15464 1.62e+04 23352 -0.1023
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# awk '{print $5}' chr23.ped | sed '1i sex' | paste - chr23_3.het | awk '$1 == 1 && $NF < 0.8'
root@DESKTOP-1N42TVH:/home/test/GWA_tutorial/1_QC_GWAS/test# awk '{print $5}' chr23.ped | sed '1i sex' | paste - chr23_3.het | awk '$1 == 2 && $NF > 0.2'
2 1349 NA10854 6632 4748 6651 0.99 ## 问题个体
标签：plink,--,sex,QC,chr23,test,home,DESKTOP 来源： https://www.cnblogs.com/liujiaxin2018/p/16471954.html