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plink 软件中 --reference-allele 参数 用于设定参考等位基因

作者:互联网

 

001、

root@DESKTOP-1N42TVH:/home/test4# ls                 ## 测试数据
outcome.map  outcome.ped
root@DESKTOP-1N42TVH:/home/test4# cat outcome.map 
1       SNP1    0       55910
1       SNP2    0       85204
1       SNP3    0       122948
1       SNP4    0       203750
1       SNP5    0       312707
1       SNP6    0       356863
1       SNP7    0       400518
1       SNP8    0       487423
root@DESKTOP-1N42TVH:/home/test4# cat outcome.ped
DOR     1       0       0       0       -9      C G     C C     T T     G G     A G     A A     G G     G C
DOR     2       0       0       0       -9      C C     G C     G G     G G     G G     A A     A G     C C
DOR     3       0       0       0       -9      G G     C C     G G     G G     A A     A A     A G     G C
DOR     4       0       0       0       -9      G G     C C     T G     T G     G G     A A     G G     G G
DOR     5       0       0       0       -9      G G     C C     G G     T 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
root@DESKTOP-1N42TVH:/home/test4# plink --file outcome --make-bed --out test &> /dev/null  ## 转二进制
root@DESKTOP-1N42TVH:/home/test4# ls
outcome.map  outcome.ped  test.bed  test.bim  test.fam  test.log  test.nosex
root@DESKTOP-1N42TVH:/home/test4# cat test.bim
1       SNP1    0       55910   C       G
1       SNP2    0       85204   G       C
1       SNP3    0       122948  T       G
1       SNP4    0       203750  T       G
1       SNP5    0       312707  A       G
1       SNP6    0       356863  0       A
1       SNP7    0       400518  A       G
1       SNP8    0       487423  G       C
root@DESKTOP-1N42TVH:/home/test4# awk '{OFS = "\t"; print $2, $5}' test.bim | sed -e '1 s/.$/G/' -e '2 s/.$/C/' > a.txt
root@DESKTOP-1N42TVH:/home/test4# cat a.txt    ## 生成--reference-allele 参数需要文件,修改了前两个SNP的reference alleles
SNP1    G
SNP2    C
SNP3    T
SNP4    T
SNP5    A
SNP6    0
SNP7    A
SNP8    G

 

002、测试命令

root@DESKTOP-1N42TVH:/home/test4# ls
a.txt  outcome.map  outcome.ped  test.bed  test.bim  test.fam  test.log  test.nosex
root@DESKTOP-1N42TVH:/home/test4# plink --bfile test --reference-allele a.txt --make-bed --recode tab --out result &> /dev/null
root@DESKTOP-1N42TVH:/home/test4# ls
a.txt        outcome.ped  result.bim  result.log  result.nosex  test.bed  test.fam  test.nosex
outcome.map  result.bed   result.fam  result.map  result.ped    test.bim  test.log
root@DESKTOP-1N42TVH:/home/test4# cat test.bim   ## 原始reference allele
1       SNP1    0       55910   C       G
1       SNP2    0       85204   G       C
1       SNP3    0       122948  T       G
1       SNP4    0       203750  T       G
1       SNP5    0       312707  A       G
1       SNP6    0       356863  0       A
1       SNP7    0       400518  A       G
1       SNP8    0       487423  G       C
root@DESKTOP-1N42TVH:/home/test4# cat a.txt       ## 计划改变为的reference allele,改变SNP1、SNP2
SNP1    G
SNP2    C
SNP3    T
SNP4    T
SNP5    A
SNP6    0
SNP7    A
SNP8    G
root@DESKTOP-1N42TVH:/home/test4# cat result.bim       ## 修改结果
1       SNP1    0       55910   G       C
1       SNP2    0       85204   C       G
1       SNP3    0       122948  T       G
1       SNP4    0       203750  T       G
1       SNP5    0       312707  A       G
1       SNP6    0       356863  0       A
1       SNP7    0       400518  A       G
1       SNP8    0       487423  G       C
root@DESKTOP-1N42TVH:/home/test4# cat outcome.ped    ## 对比命令前后ped文件
DOR     1       0       0       0       -9      C G     C C     T T     G G     A G     A A     G G     G C
DOR     2       0       0       0       -9      C C     G C     G G     G G     G G     A A     A G     C C
DOR     3       0       0       0       -9      G G     C C     G G     G G     A A     A A     A G     G C
DOR     4       0       0       0       -9      G G     C C     T G     T G     G G     A A     G G     G G
DOR     5       0       0       0       -9      G G     C C     G G     T 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
root@DESKTOP-1N42TVH:/home/test4# cat result.ped
DOR     1       0       0       0       -9      G C     C C     T T     G G     A G     A A     G G     G C
DOR     2       0       0       0       -9      C C     C G     G G     G G     G G     A A     A G     C C
DOR     3       0       0       0       -9      G G     C C     G G     G G     A A     A A     A G     G C
DOR     4       0       0       0       -9      G G     C C     T G     T G     G G     A A     G G     G G
DOR     5       0       0       0       -9      G G     C C     G G     T 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

 

标签:1N42TVH,plink,reference,--,DESKTOP,DOR,test,home,test4
来源: https://www.cnblogs.com/liujiaxin2018/p/16479000.html