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

jimmikeself

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

Geraldine_VdAuwera

As indicated on the homepage or downloads page, the latest version is 2.1-13. FYI, we advertise new versions on our mailing list and on twitter (@gatk_dev) to help people stay up-to-date.

Geraldine_VdAuwera

Can you tell me what version you're using and post your command line?

jimmikeself

Geraldine, Thank you for quick response. The version is version 1.6-11-g3b2fab9 on Linux 64 -Jim

Geraldine_VdAuwera

That's a pretty old version, you should really upgrade to the latest version. It will very probably fix your problem.

jimmikeself

I thought that 1.6-11-g3b2fab9 is the most recent stable release of GATK. What is the stable release version?

Thanks, -Jim