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Haplotype Caller and multiple of 3 DP?

YannickRenaudYannickRenaud Posts: 3Member
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

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,781Administrator, GATK Dev admin

    Hi Yannick,

    We've never seen this pattern, so it might just be a coincidence. If you see this happening again with other datasets, or if others observe it too, we'll take a closer look, but until then I'm afraid we can't give this any attention.

    Geraldine Van der Auwera, PhD

  • YannickRenaudYannickRenaud Posts: 3Member

    Thanks, I'll see if we get it with another dataset.

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