仅使用 awk :

$ awk 'NR==FNR{a[$1,$2,$3]; next} !(($1,$2,$3) in a)' file2 file1
chr1    9997    10330   HumanGM18558_peak_1     150     .       10.78887        18.86368        15.08777        100
chr1    15966215        15966638        HumanGM18558_peak_3    81      .       7.61567 11.78841        8.17169 200

• NR == FNR 这仅适用于第一个文件，在本示例中为 file2
• a [$ 1，$ 2，$ 3] 根据前三个字段创建键，如果两个文件之间的间距完全相同，则可以简单地使用 $ 0 $ 1，$ 2，$ 3
• next 跳过其余命令并处理下一行输入
• ($ 1，$ 2，$ 3)在一个中，以检查 file1 的前三个字段是否作为键出现在数组 a 中.然后反转条件.
• NR==FNR this will be true only for the first file, which is file2 in this example
• a[$1,$2,$3] create keys based on first three fields, if spacing is exactly same between the two files, you can simply use $0 instead of $1,$2,$3
• next to skip remaining commands and process next line of input
• ($1,$2,$3) in a to check if first three fields of file1 is present as key in array a. Then invert the condition.

这是另一种编写方法(感谢Ed Morton)

Here's another way to write it (thanks to Ed Morton)

awk '{key=$1 FS $2 FS $3} NR==FNR{a[key]; next} !(key in a)' file2 file1