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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

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