How To Interpret The Flag Field In The Sam Specification

Question

[deepthithomaskannan]

Hi all ,

I created a sam file and converted it to bam file using samtools.

One of the record in bam file is :

HWI-ST1162:72:D0PMMACXX:5:1104:10496:88597      16      gi|355477192|ref|NC_007299.5|   1       255     101M    *       0       0       TACCCCACTCACACTTATGGATAGATCAACTAAACAGAAAATTAACAAGGAAAAAAAAAACAAAAAAAACATGTATCTATAAAGCTCACTAAAGGAAAGCA        05DDDDCDDCDDDDDDDDDDDCDCCADDDCDDDEDDEDEEEEDDDDDDDDDDHJJJJJJIJJJJJJJJIIJJJJJIJGJJJJJJIIHGHHHHHFFFFFCCC        XA:i:1  MD:Z:60A33C6    RG:Z:D0PMMACXX:IT27.48-3        NM:i:2

What does the second field means? What may be the possible values for second field of a bam file. In one paper I read it as a flag. But I could not find the explanation for value 0 and 16 .

Thanks, Deeps

[iyer.laxman4]

Answer is fine but it is not working so sorry

[Devon Ryan]

What answer isn't working? Istvan's link to the "Explain SAM Flags" still works, as does that site.

Answer 1

[Istvan Albert]

In a nutshell any integer number may be entered although some of these number may have contradictory or overlapping effects.

The best way to visualize the flag fields is via Explain SAM Flags web interface.

To also answer your question each flag corresponds to a bit set in a binary representation of the number

1 -> 00001
2 -> 00010
4 -> 00100
8 -> 01000

Then if you need to set flags 1 and 4 then the bits that will be set are 00101 and the integer flag would be 5

[JC]

great tool the "Explain SAM Flags"!, I expended A LOT of time understanding the combinations

Answer 2

[swbarnes2]

I think some of the confusion happens because we call them binary flags, but they are displayed in decimal in the .sam file, but when they are explained in the SAM specification document, they are displayed in hexadecimal.

Answer 3

[-_-]

For even faster and more handy interpretation of the flag, try http://www.samformat.info/#/flag

[Istvan Albert]

this is neat but IMO it should work both ways, selecting rows should produce numbers.

building a number out of the desired flags is just as often needed

[-_-]

Agreed, added that feature, too and improved the binary illustration.

[Istvan Albert]

nice, I'll add this to my lecture notes ;-)

Answer 4

[Damian Kao]

I wrote a blog post about this a while back: http://blog.nextgenetics.net/?e=18

It might be more detail than you need to know about how bitwise flags work.

[Istvan Albert]

excellent summary - your blog was not listed in the planet feed - problem rectified!

Answer 5

[JC]

In short: 0 is a single-end read mapped in the forward strand, 16 is in the reverse strand. Check all the details about the bitwise flag in the samtools manual: http://samtools.sourceforge.net/samtools.shtml and SAM format description: http://samtools.sourceforge.net/SAM1.pdf