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Old 08-18-2016, 03:19 AM   #1
LeonDK
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Location: Denmark

Join Date: Sep 2014
Posts: 69
Default Calculate the proportion of missing data per sample from VCF file

I have a VCFv4.2 (Sanger-imputation-service genotype data) file and I need to calculate the proportion of missing data per sample.

Each sample is encoded like so:
Code:
GT:ADS:DS:GP
0|0:0.25,0.15:0.4:0.6375,0.325,0.0375
I am uncertain as to how 'missing' is identified - Any suggestions?
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