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too many PL values
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