Used in: gor only

BAMFLAG¶

The BAMFLAG command expands the FLAG bitmap column into multiple Boolean (1/0) columns. This makes the parameters in the FLAG bitmap easier to read.

The table below shows a list of the different parameters and their corresponding bit in the flag value.

The Flag Column as expanded by BAMFLAG¶
#	Binary	Decimal	Hexadecimal	Description
1	1	1	0x1	Read paired
2	10	2	0x2	Read mapped in proper pair
3	100	4	0x4	Read unmapped
4	1000	8	0x8	Mate unmapped
5	10000	16	0x10	Read reverse strand
6	100000	32	0x20	Mate reverse strand
7	1000000	64	0x40	First in pair
8	10000000	128	0x80	Second in pair
9	100000000	256	0x100	Not primary alignment
10	1000000000	512	0x200	Read fails platform/vendor quality checks
11	10000000000	1024	0x400	Read is PCR or optical duplicate
12	100000000000	2048	0x800	Supplementary alignment

Usage¶

gor file.bam | BAMFLAG [ -v ]

`-v`	Use verbose column names.