Hello,
On Thu, Mar 03, 2016 at 05:04:05PM -0500, Andrew Bjonnes wrote:
> An example is a record with FLAG = 153 = 0b000010011001. This corresponds
> to the following flags set:
> 0x1 = 0b000000000001: template having multiple segments in sequencing
> 0x8 = 0b000000001000: next segment in the template unmapped
> 0x10 = 0b000000010000: SEQ being reverse complemented
> 0x80 = 0b000010000000: the last segment in the template
>
> So, as a contrived example, if you wanted to view only records where SEQ is
> reverse complemented (16 = 0x10 = 0b000000010000) and the read is marked as
> an optical or PCR duplicate (1024 = 0x400 = 0b010000000000), you would
> simply add these together (1040 = 0b010000010000) and use this value: samtools
> view -f 1040 ...
For ease of use note that samtools has a flags sub-command. With no
other arguments it lists the flags. Given arguments it does the
conversions for you. Eg:
[nfs_j/jkb]; samtools flags
About: Convert between textual and numeric flag representation
Usage: samtools flags INT|STR[,...]
Flags:
0x1 PAIRED .. paired-end (or multiple-segment) sequencing
technology
0x2 PROPER_PAIR .. each segment properly aligned according to the
aligner
0x4 UNMAP .. segment unmapped
0x8 MUNMAP .. next segment in the template unmapped
0x10 REVERSE .. SEQ is reverse complemented
0x20 MREVERSE .. SEQ of the next segment in the template is
reversed
0x40 READ1 .. the first segment in the template
0x80 READ2 .. the last segment in the template
0x100 SECONDARY .. secondary alignment
0x200 QCFAIL .. not passing quality controls
0x400 DUP .. PCR or optical duplicate
0x800 SUPPLEMENTARY .. supplementary alignment
[nfs_j/jkb]; samtools flags REVERSE,DUP
0x410 1040 REVERSE,DUP
[nfs_j/jkb]; samtools flags 1040
0x410 1040 REVERSE,DUP
--
James Bonfield ([email protected]) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
--
The Wellcome Trust Sanger Institute is operated by Genome Research
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