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why are the PL (Phred-scaled likelihoods) values missing from the genotype info?

jimmikeselfjimmikeself Member
edited October 2012 in Ask the GATK team

The printed values missed the PL value, for examples, the format is:

GT:AD:DP:GQ:PL
['0/2', '1,0,10', '11', '8.12']
['0/2', '211,39,0', '250', '99']
['0/1', '10,1', '11', '14.38']
['0/1', '4,2', '4', '24.38']    
['0/0', '27,0', '27', '78.26']
['1/1', '164,2', '183', '99']
['0/1', '242,1', '249', '99']
['0/1', '225,0', '233', '99']
['0/0', '84,5', '82', '81.18']

For every case, the PL value is missing.
It happens most often when there are more than one alternative alleles.

Thank you,

Jim

Post edited by Geraldine_VdAuwera on
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