the format of SAM

[biocc]

hello, I do not understand the FLAG in SAM. could someone explain it. In paper " The Sequence Alignment/Map format and SAMtools", it says that According to FLAG
163(=1+2+32+ 128), the read mapped to position 7 is the second read in
the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to
37 on the reverse strand (32).
and each bit in the FLAG field is defined as:
Flag Description
0x0001 Paired in sequencing
0x0002 Mapped in proper read pair
0x0004 Query unmapped
0x0008 Mate unmapped
0x0010 Strand of the query (1 for reverse)
0x0020 Strand of the mate (1 for reverse)
0x0040 First read in the pair
0x0080 Second read in the pair
0x0100 Secondary alignment
0x0200 QC failure
0x0400 Optical or PCR duplicates
how to explain it. thanks in advance.

[nicolallias]

Hi,
Play with : http://picard.sourceforge.net/explain-flags.html
163(=1+2+32+ 128) is in decimal
0x00.. are hexadecimal (base 16, not 10)

0,0010 is equivalent to the decimal 16^1 so 16.

[kmcarr]

biocc,

I created a little cheat sheet for myself to be able to quickly decipher the flags in a SAM output. The bottom row lists decimal values as they would appear in the FLAG field of the SAM file and the top row provides the interpretation of the that FLAG value. In between shows the specific elements which added up to the final value (as you showed in your example.

[gerald2545]

you can also use the samtools view -X option which transforms the flag to a string, human readable.
samtools view -? for details

Gerald

[biocc]

thanks for everyone. i understand the FLAG now.

[mimi_lupton]

Dear all,
Thanks for the posts above, that was exactly my question. I also have a additional question. I am trying to do remove duplicates with PICARD. I get an error because my input file has secondary alignments and MarkDuplicates does not take into account the secondary alignment flag. Anyone have an idea of how to remove them?

Any help would be really appreciated

[michaeltmccarthy]

biocc,

I created a little cheat sheet for myself to be able to quickly decipher the flags in a SAM output. The bottom row lists decimal values as they would appear in the FLAG field of the SAM file and the top row provides the interpretation of the that FLAG value. In between shows the specific elements which added up to the final value (as you showed in your example.

Brilliant!