以下这段翻译自SAMv1.pdf
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以下几个选项计算结果一样
-c -f1 =-c -F12
-c -f2 =-c -f2 -F4 = -c -f2 -F12
-c -F12=-c -F524 # 0x4 + 0x8 + 0x200
-c -F4 = -c -F516
-c -F260=-c -F772 # 0x4 + 0x100 + 0x200
-c -F268=-c -F780 # 0x4 + 0x8 + 0x100 + 0x200
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samtools flagstat中几个指标的计算方法
$ samtools flagstat H1650RNA_S12.hg19.bam
28400342 + 0 in total (QC-passed reads + QC-failed reads) # -c
2924468 + 0 secondary # -c -f0x100
0 + 0 supplementary
0 + 0 duplicates
28188350 + 0 mapped (99.25%:-nan%) # -c -F4
25475874 + 0 paired in sequencing
12737937 + 0 read1
12737937 + 0 read2
21967790 + 0 properly paired (86.23%:-nan%) # -c -F268 -f2
25087116 + 0 with itself and mate mapped # -c -F268
176766 + 0 singletons (0.69%:-nan%)
1502110 + 0 with mate mapped to a different chr
760983 + 0 with mate mapped to a different chr (mapQ>=5)