New Pileup Output

Question

[Lee Katz]

The pileup output description is different than the output I am getting now. Could anyone help me with a definition of each column? http://samtools.sourceforge.net/pileup.shtml

This is a line from my output. It has additional columns when compared against the original description.

1  621 T    G 159   159 36   74 g$g$gggggGGgggggggGGggGGGGgGGgGggGGgGGgggGGgggGGgggGGggGggGgGgGgGggGggggGGgG  !!!!***A:2223222:32238:8273232237522532222222322222922222322222222233322'!

[Russh]

strange, which program did you use?

[Lee Katz]

I used the pileup command. I think that Sean Davis answered my question.

Answer 1

[Sean Davis]

See here:

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

Note the section under pileup where there are more details given about the extra columns. Also, note the pileup is deprecated and will be soon dropped from samtools, so consider switching to mpileup for variant calling.