plink 软件中 --impute-sex 参数
plink 软件中--impute-sex参数：基因基因型信息推断性别（x染色体--het参数的F值，female: F < 0.2; male: F > 0.8）， 并写入数据。
001、计算f值
root@DESKTOP-1N42TVH:/home/test5# ls outcome.map outcome.ped root@DESKTOP-1N42TVH:/home/test5# cat outcome.map 23 s64199.1 0 55910 23 OAR19_64675012.1 0 85204 23 OAR19_64715327.1 0 122948 23 OAR19_64803054.1 0 203750 23 DU281551_498.1 0 312707 23 s18939.1 0 356863 23 OAR1_88143.1 0 400518 23 s09912.1 0 487423 root@DESKTOP-1N42TVH:/home/test5# cat outcome.ped ## ped文件第5列性别信息0， 表示未知 DOR 1 0 0 0 -9 A G C C G G G G A G C A G G G C DOR 2 0 0 0 -9 A A G C T T G G G G C C A G C C DOR 3 0 0 0 -9 G G C C G G 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 A A A G C C root@DESKTOP-1N42TVH:/home/test5# plink --file outcome --het --chr-set 30 --out test1 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 test1.log. Options in effect: --chr-set 30 --file outcome --het --out test1 16007 MB RAM detected; reserving 8003 MB for main workspace. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (8 variants, 10 samples). --file: test1-temporary.bed + test1-temporary.bim + test1-temporary.fam written. 8 variants loaded from .bim file. 10 samples (0 males, 0 females, 10 ambiguous) loaded from .fam. Ambiguous sex IDs written to test1.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 samples pass filters and QC. Note: No phenotypes present. --het: 8 variants scanned, report written to test1.het . root@DESKTOP-1N42TVH:/home/test5# ls outcome.map outcome.ped test1.het test1.log test1.nosex root@DESKTOP-1N42TVH:/home/test5# cat test1.het ## 最后一列F值 FID IID O(HOM) E(HOM) N(NM) F DOR 1 4 5.7 8 -0.7391 DOR 2 6 5.7 8 0.1304 DOR 3 6 5.7 8 0.1304 DOR 4 8 5.7 8 1 DOR 5 6 5.7 8 0.1304 DOR 6 8 5.7 8 1 DOR 7 7 5.7 8 0.5652 DOR 9 7 5.7 8 0.5652 DOR 10 6 5.7 8 0.1304 DOR 11 6 5.7 8 0.1304
002、使用--impute-sex参数参数推测性别
root@DESKTOP-1N42TVH:/home/test5# ls outcome.map outcome.ped test1.het test1.log test1.nosex root@DESKTOP-1N42TVH:/home/test5# plink --file outcome --impute-sex --recode tab --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 outcome --impute-sex --out test2 --recode tab 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: test2-temporary.bed + test2-temporary.bim + test2-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 test2.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. --impute-sex: 8 Xchr and 0 Ychr variant(s) scanned, 8/10 sexes imputed. Report written to test2.sexcheck . --recode ped to test2.ped + test2.map ... done. root@DESKTOP-1N42TVH:/home/test5# ls outcome.map outcome.ped test1.het test1.log test1.nosex test2.log test2.map test2.nosex test2.ped test2.sexcheck root@DESKTOP-1N42TVH:/home/test5# cat test2.ped ## 性别推测结果为第5列 DOR 1 0 0 2 -9 A G C C G G G G A G C A G G G C DOR 2 0 0 2 -9 A A G C T T G G G G C C A G C C DOR 3 0 0 2 -9 G G C C G G G G G G A A A G G C DOR 4 0 0 1 -9 G G C C G G G G G G A A G G G G DOR 5 0 0 2 -9 G G C C G G G G G G A A A G G C DOR 6 0 0 1 -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 2 -9 G G G C G G G G G G A A A G C C DOR 11 0 0 2 -9 G G C C G G G G A G A A A G C C root@DESKTOP-1N42TVH:/home/test5# cat test1.het ## 跟f值一致 FID IID O(HOM) E(HOM) N(NM) F DOR 1 4 5.7 8 -0.7391 DOR 2 6 5.7 8 0.1304 DOR 3 6 5.7 8 0.1304 DOR 4 8 5.7 8 1 DOR 5 6 5.7 8 0.1304 DOR 6 8 5.7 8 1 DOR 7 7 5.7 8 0.5652 DOR 9 7 5.7 8 0.5652 DOR 10 6 5.7 8 0.1304 DOR 11 6 5.7 8 0.1304
