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!

Powered by Vanilla. Made with Bootstrap.
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

Haplotype Caller and multiple of 3 DP?

YannickRenaudYannickRenaud Member Posts: 3
edited August 2013 in Ask the GATK team

Hello All,

I'm a new user of haplotypecaller. I am currently comparing it to unifiedgenotyper and samtools.
When I do a count of SNPs for all DPs, it looks like the is a multiple of 3 issues.
There seems to be a lot more SNPs with a DP of 3, 6, 9, ... compared to 1, 2, 4, 5, 7, 8 ....

DP #ofSNP
1 43
2 41
3 105
4 24
5 18
6 232
7 38
8 66
9 3749

I was wondering if this was a normal behavior and what caused it.

Yannick

Post edited by Geraldine_VdAuwera on

Answers

Sign In or Register to comment.