The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
I've run the GATK best practices pipeline up through VQSR and have the recalibrated variants in a VCF file. Because I'm analyzing pedigree samples, I'm now attempting to run CalculateGenotypePosteriors. When I do this, I get the following error:
ERROR MESSAGE: Variant does not contain the same number of MLE allele counts as alternate alleles for record at 1:768589
However, when I looked at that variant in the recalibrated VCF file, I see that MLEAC=1, AC=1, and I can confirm that there is only one sample that is heterozygous, so both AC and MLEAC are correct.
Might this be a bug?