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Old 04-23-2015, 05:28 AM   #1
Joe Dever
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Location: EU

Join Date: Mar 2015
Posts: 3
Default strange GT values from GATK

Hi,

I am looking at some data processed through Illumina's BWA+GATK pipeline.

I found some funny GT values, like:

./. 1/1 1/1 1/1 ./. 1

. . 1 . . .

1 ./. 0/1 ./. ./. ./.

1 1 1/1 1 ./. ./.

I am familiar with 1/1, 0/1, 0/2, etc., but I don't understand what "." and "1" mean. Can anybody help me understand this output?
Thanks!
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