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Old 03-11-2014, 05:17 PM   #1
Elsie
Member
 
Location: Australia

Join Date: Mar 2011
Posts: 85
Default Reading a vcf - genotypes

Hi, I am trying to understand the genotype calls in my vcf, a trio.
Looking at one variant of interest, the calls are:
Dad Mum Kid
0/2 2/1 1/1

How can the kid be 1/1?
The full information is:

FORMAT
GT:ADP:GQ:PL

Dad
0/2:9,3,0:16:19.63:134,0,98,27,20,47

Mum
145 2/1:8,4,0:20:15.38:197,15,52,44,0,41

Child
1/1:7,2,0:11:1.37:113,31,61,9,1,0


Thanks for any help.
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Old 03-12-2014, 02:58 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Note the GQ value, which is quite low for the child. You might consider filtering by quality.

You will run into this sort of thing on occasion. The general causes are (1) sequencing error (2) genotype call error (3) sample swap (this should be pretty obvious though) (4) non-paternity. The last one is more common than you would think (1-3% of cases where there's otherwise no dispute of paternity), though you'll again end up with a lot of sites like this.
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