samtools output format

[bair]

Samtools protocol and FAQ explain how to use samtools, but both not explain the output format of each functions.

For example, samtools pileup -c to output MAQ cns format, searching and reading MAQ manual, I did not find the answer.

Anybody can help me?

[bair]

maq snp file looks like:

chrX 58578121 T G 74 27 1.19 53 62 K 255 T
chrX 58578144 C A 126 33 4.06 53 62 N 255 N
chrX 61677006 T C 27 9 3.00 53 30 Y 110 T

SNP file got from samtools pileup -c looks like

chrX 58568462 a W 10 10 60 7 ......^~T ZZ[Z[[[
chrX 58568463 a W 10 10 60 7 ..T.... [Z[Z[[[
chrX 58572756 t A 39 39 60 4 AAAA Z[[[
chrX 58572850 c G 39 39 60 4 gggg [W[[

The output are quite different.

MAQ manual explains each of the output columns, how to explain the columns in samtools output?

[lh3]

Aren't the following pages explain the format?

http://sourceforge.net/apps/mediawik..._pileup_output.

http://samtools.sourceforge.net/samtools.shtml

In addition, I do not remember I have ever said the "pileup -c" gives MAQ format. If you could point me to that part in documentation, I will change it.

[bair]

Thank you lh3, I just got it. Also get help from Galaxy website.
ttp://main.g2.bx.psu.edu/


samtools pileup option

-f FILE reference sequence in the FASTA format
-c output the maq consensus sequence
-v print variants only (for -c)

I think with option c, samtools outputs kind of maq format.

[lh3]

"MAQ consensus sequence" is different from "MAQ output format". Anyway, I will consider to change that if I still remember this. Thank you.