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too many PL values

zevkronenbergzevkronenberg Member
edited March 2016 in Ask the GATK team

Greetings,

I've run best practices for HC. Merged my populations into seven GVCFs and genotyped.

After trying to run BEAGLE I see that there are some genotypes that have too many PL values.

Has anyone run into this?

Doesn't this break VCF spec?

Exception in thread "main" java.lang.IllegalArgumentException: unexpected number of PL subfields: 0,21,315,21,315,315
1 840113 . T C 1098.14 PASS AC=7;AF=0.013;AN=528;BaseQRankSum=-7.400e-01;ClippingRankSum=-4.030e-01;DP=7058;ExcessHet=7.7159;FS=11.599;InbreedingCoeff=-0.0435;MLEAC=7;MLEAF=0.013;MQ=58.26;MQ0=0;MQRankSum=-6.300e-01;QD=4.24;ReadPosRankSum=-1.517e+00;SOR=0.991;VQSLOD=-2.012e+00;culprit=QD;NEGATIVE_TRAIN_SITE GT:AB:AD:DP:GQ:PGT:PID:PL

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