方法1

使用软件illumina2preGS，

功能是：仅读取 AB 代码并生成整型变量 0、1、2 或 5 用于缺失

输入文件是FinalReport和SNP_Map.txt文件
注意这SNP_Map.txt文件是以TAB分割。
在liunx中将空格分割改为TAB分割命令：

sed -i 's/\s\+/\t/g' SNP_Map.txt

转换文件格式命令

./illumina2preGS --snpfile A3672_Batch_01_528_samples_Final_Report.txt --mapfile SNP_Map.txt --genome 1 --sortmap

一些OPTION说明

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输出文件结果

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例子

---------------------------------------------------- 
 |                  illumina2preGS                    |
 |          Converts FinalReport files from           |
 |         Illumina GenomeStudio into files           |
 |       suitables for BLUPF90 family programs        |
 |                                                    |
 |                2011 - Version 1.31                 |
 |           (Last update:  Nov 05, 2021)             |
 |                                                    |
 |             INIA Las Brujas, Uruguay               |
  ---------------------------------------------------- 

 Options
    --snpfile A3672_Batch_01_528_samples_Final_Report.txt
    --mapfile SNP_Map.txt
    --genome 1
    --sortmap

 Current options
   Genome: bovine    
     X   ->  30
     Y   ->  31
     MT  ->  32
     0   ->  33
   Size for sample ID: 19
 
   MAP file: SNP_Map.txt
     Column number for SNP Name:   1
     Column number for Chromosome: 2
     Column number for Position:   3
 
   SNP file: A3672_Batch_01_528_samples_Final_Report.txt
     Column number for SNP Name:   1
     Column number for Sample Id:  2
     Column number for AB code:    5
 
 Number of snps from Mapfile "SNP_Map.txt": 777962



 Number of lines read:        409985974
 Number of samples:           527
 Number of converted samples: 527
 Number of wrong samples:     0

 SNP order: by chr,position

 Genotype Codes: indicate number of copies of B allele
    0 -> AA
    1 -> AB or BA
    2 -> BB
    5 -> No Call

 Output files
   Map file: "snp_map"
   SNP file: "snps2pregs"