samtools flagstat统计bam文件比对结果
$ samtools flagstat
Usage: samtools flagstat [options] <in.bam>
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-@, --threads INT
Number of additional threads to use [0]
$ samtools flagstat -@ 8 EV-1_HISAT2.bam
59306432 + 0 in total (QC-passed reads + QC-failed reads)
4546096 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
55162761 + 0 mapped (93.01% : N/A)
54760336 + 0 paired in sequencing
27380168 + 0 read1
27380168 + 0 read2
48652166 + 0 properly paired (88.85% : N/A)
49197764 + 0 with itself and mate mapped
1418901 + 0 singletons (2.59% : N/A)
106592 + 0 with mate mapped to a different chr
82634 + 0 with mate mapped to a different chr (mapQ>=5)
