samtools flagstat参数对比对的bam文件进行统计

 

001、命令

samtools flagstat sample_name.sorted.bam > sample_name.flagstat.txt

 

 

a、生成的文件是一个包含16行的文本文件：

 

002、

(base) [b20223040323@admin2 workdir]$ cat Asiatic1.flagstat.txt      ## 查看统计结果
622520785 + 0 in total (QC-passed reads + QC-failed reads)
620876200 + 0 primary
1644585 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
621864067 + 0 mapped (99.89% : N/A)
620219482 + 0 primary mapped (99.89% : N/A)
620876200 + 0 paired in sequencing
310438100 + 0 read1
310438100 + 0 read2
612737342 + 0 properly paired (98.69% : N/A)
620022610 + 0 with itself and mate mapped
196872 + 0 singletons (0.03% : N/A)
5577184 + 0 with mate mapped to a different chr
2767972 + 0 with mate mapped to a different chr (mapQ>=5)

 。

 

003、