plink软件删除非ATCG的位点
1、测试数据
root@PC1:/home/test# ls test.map test.ped root@PC1:/home/test# cat test.map ## 测试数据中一共包含有5个位点 2 snp1 0 209225353 2 snp2 0 209233002 2 snp3 0 209237381 13 snp4 0 63047423 13 snp5 0 63047428 root@PC1:/home/test# cat test.ped ## 最后两个位点中包含有I和D 3998953053 idv1 0 0 0 -9 A A A A A A D I D I 3998953053 idv2 0 0 0 -9 A A G A A A D I D I 3998953053 idv3 0 0 0 -9 A A A A A A I I I I 3998953053 idv4 0 0 0 -9 C A G A A A I I I I 3998953053 idv5 0 0 0 -9 A A G A A A I I I I 3998953053 idv6 0 0 0 -9 C C G A A A I I I I
2、使用plink软件删除包含I和D的位点
root@PC1:/home/test# ls test.map test.ped root@PC1:/home/test# cat test.map 2 snp1 0 209225353 2 snp2 0 209233002 2 snp3 0 209237381 13 snp4 0 63047423 13 snp5 0 63047428 root@PC1:/home/test# cat test.ped 3998953053 idv1 0 0 0 -9 A A A A A A D I D I 3998953053 idv2 0 0 0 -9 A A G A A A D I D I 3998953053 idv3 0 0 0 -9 A A A A A A I I I I 3998953053 idv4 0 0 0 -9 C A G A A A I I I I 3998953053 idv5 0 0 0 -9 A A G A A A I I I I 3998953053 idv6 0 0 0 -9 C C G A A A I I I I root@PC1:/home/test# plink --file test --snps-only just-acgt --recode tab --out result ## 使用--snps-only just-acgt参数删除非actg位点 PLINK v1.90b6.24 64-bit (6 Jun 2021) www.cog-genomics.org/plink/1.9/ (C) 2005-2021 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to result.log. Options in effect: --file test --out result --recode tab --snps-only just-acgt 15967 MB RAM detected; reserving 7983 MB for main workspace. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (5 variants, 6 people). --file: result-temporary.bed + result-temporary.bim + result-temporary.fam written. 3 out of 5 variants loaded from .bim file. 6 people (0 males, 0 females, 6 ambiguous) loaded from .fam. Ambiguous sex IDs written to result.nosex . Using 1 thread (no multithreaded calculations invoked). Before main variant filters, 6 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is exactly 1. 3 variants and 6 people pass filters and QC. Note: No phenotypes present. --recode ped to result.ped + result.map ... done. root@PC1:/home/test# ls result.log result.map result.nosex result.ped test.map test.ped root@PC1:/home/test# cat result.map ##查看结果 2 snp1 0 209225353 2 snp2 0 209233002 2 snp3 0 209237381 root@PC1:/home/test# cat result.ped ## 查看结果 3998953053 idv1 0 0 0 -9 A A A A A A 3998953053 idv2 0 0 0 -9 A A G A A A 3998953053 idv3 0 0 0 -9 A A A A A A 3998953053 idv4 0 0 0 -9 C A G A A A 3998953053 idv5 0 0 0 -9 A A G A A A 3998953053 idv6 0 0 0 -9 C C G A A A
