The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at http://bit.ly/2i4mGxz

how to translate the output of the Pileup tool

ChinaMember Posts: 18

Hi,there.I have just run the Pileup tool and get the output of it. It is a txt file with 5 columns. The first 3 columns are numbers, and the left two are base symbols.What do the 5 columns mean?

Tagged:

Geraldine Van der Auwera, PhD

• ChinaMember Posts: 18
edited September 2013

Thank you so much.I have read the documentation, But I don't quite understand why there is only one base in the fifth column(read bases). This is two row in my output.txt. according to the documentation, the 5 columns represent chromosome name, coordinate, reference base, read bases, and read qualities, respectively.

1 563666 T T A
1 12242 T T ?


Each row represent a position, For example, if the depth of the 1st position is 300, then there should be 300 bases which have been read in this position, but in the output.txt, there is only one base in the fifth column.
So I don't quite understand the output of pileup.

Post edited by Geraldine_VdAuwera on