标签：shell plink NA PC1 result home test 格式
001、测试数据
root@PC1:/home/test# ls
mdp_genotype_test.hmp.txt record.sh
root@PC1:/home/test# head -n 5 mdp_genotype_test.hmp.txt | cut -f 1-13 ## 测试数据
rs alleles chrom pos strand assembly center protLSID assayLSID panel QCcode 33-16 38-11
PZB00859.1 A/C 1 157104 + AGPv1 Panzea NA NA maize282 NA CC CC
PZA01271.1 C/G 1 1947984 + AGPv1 Panzea NA NA maize282 NA CC GG
PZA03613.2 G/T 1 2914066 + AGPv1 Panzea NA NA maize282 NA GG GG
PZA03613.1 A/T 1 2914171 + AGPv1 Panzea NA NA maize282 NA TT TT
root@PC1:/home/test# cat record.sh ## 转换脚本
#!/bin/bash
columns=$(head -n 1 $1 | awk '{print NF}')
for i in $(seq 12 $columns); do cut -f $i $1 | paste -d "\t" -s | sed 's/\r//g; s/NN/00/g; s/\t./&\t/g;s/^\S\+\t/&&\t0\t0\t1\t-9\t/g' >> result.ped; done
sed 1d $1 | awk '{OFS = "\t"; print $3, $1, 0, $4}' > result.map
root@PC1:/home/test# ls mdp_genotype_test.hmp.txt record.sh root@PC1:/home/test# bash record.sh mdp_genotype_test.hmp.txt ## 格式转换 root@PC1:/home/test# ls mdp_genotype_test.hmp.txt record.sh result.map result.ped root@PC1:/home/test# plink --file result --recode ## 测试转换结果 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 plink.log. Options in effect: --file result --recode 15969 MB RAM detected; reserving 7984 MB for main workspace. .ped scan complete (for binary autoconversion). Warning: Variant 424 quadallelic; setting rarest alleles missing. Performing single-pass .bed write (3093 variants, 281 people). --file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam written. 3093 variants loaded from .bim file. 281 people (281 males, 0 females) loaded from .fam. Using 1 thread (no multithreaded calculations invoked). Before main variant filters, 281 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is 0.963828. 3093 variants and 281 people pass filters and QC. Note: No phenotypes present. --recode ped to plink.ped + plink.map ... done. root@PC1:/home/test# ls mdp_genotype_test.hmp.txt plink.log plink.map plink.ped record.sh result.map result.ped
标签：shell,plink,NA,PC1,result,home,test,格式 来源： https://www.cnblogs.com/liujiaxin2018/p/16530854.html
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