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Old 08-18-2016, 05:11 AM   #3
LeonDK
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Location: Denmark

Join Date: Sep 2014
Posts: 69
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Quote:
Originally Posted by dpryan View Post
Missing data will have ".|." or "./." as the genotype. However, since this is imputed I'm not sure how much there will be in the way of missing values (they should have been largely imputed).
Running the following on the vcf files
Code:
for f in `ls -1`; do gunzip -c $f | grep -c '\.|\.'; done
Yields nothing but zeros, so it looks like you are correct.
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